Search results for the GEO ID: GSE19392  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM528620 | GPL3921 |
|
HBEs treated with 100ul of pre trypsin media 100pre0.5_C11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 35
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 100ul of pre trypsin media
agent: pre trypsin media
dose: 100ul 1 ug/ml TPCK trypsin
time: 0.5 h
|
HBEs treated with 100ul of pre trypsin media
100pre0.5
|
| Sample_geo_accession | GSM528620
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528620/suppl/GSM528620_plate1_C11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528621 | GPL3921 |
|
HBEs treated with 100ul of pre trypsin media 100pre1.5_F12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 72
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 100ul of pre trypsin media
agent: pre trypsin media
dose: 100ul 1 ug/ml TPCK trypsin
time: 1.5 h
|
HBEs treated with 100ul of pre trypsin media
100pre1.5
|
| Sample_geo_accession | GSM528621
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528621/suppl/GSM528621_plate1_F12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528622 | GPL3921 |
|
HBEs treated with 100ul of pre trypsin media 100pre18_H4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 184
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 100ul of pre trypsin media
agent: pre trypsin media
dose: 100ul 1 ug/ml TPCK trypsin
time: 18 h
|
HBEs treated with 100ul of pre trypsin media
100pre18
|
| Sample_geo_accession | GSM528622
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528622/suppl/GSM528622_plate2_H04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528623 | GPL3921 |
|
HBEs treated with 100ul of pre trypsin media 100pre4_H9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 93
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 100ul of pre trypsin media
agent: pre trypsin media
dose: 100ul 1 ug/ml TPCK trypsin
time: 4 h
|
HBEs treated with 100ul of pre trypsin media
100pre4
|
| Sample_geo_accession | GSM528623
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528623/suppl/GSM528623_plate1_H09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528624 | GPL3921 |
|
HBEs treated with 100ul of pre trypsin media 100pre8_E3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 147
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 100ul of pre trypsin media
agent: pre trypsin media
dose: 100ul 1 ug/ml TPCK trypsin
time: 8 h
|
HBEs treated with 100ul of pre trypsin media
100pre8
|
| Sample_geo_accession | GSM528624
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528624/suppl/GSM528624_plate2_E03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528625 | GPL3921 |
|
HBEs treated with 25ul of post trypsin media 25post0.5_C8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 32
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 25ul of post trypsin media
agent: post trypsin media
dose: 25ul 1 ug/ml TPCK trypsin
time: 0.5 h
|
HBEs treated with 25ul of post trypsin media
25post0.5
|
| Sample_geo_accession | GSM528625
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528625/suppl/GSM528625_plate1_C08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528626 | GPL3921 |
|
HBEs treated with 25ul of post trypsin media 25post1.5_F9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 69
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 25ul of post trypsin media
agent: post trypsin media
dose: 25ul 1 ug/ml TPCK trypsin
time: 1.5 h
|
HBEs treated with 25ul of post trypsin media
25post1.5
|
| Sample_geo_accession | GSM528626
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528626/suppl/GSM528626_plate1_F09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528627 | GPL3921 |
|
HBEs treated with 25ul of post trypsin media 25post18_H1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 181
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 25ul of post trypsin media
agent: post trypsin media
dose: 25ul 1 ug/ml TPCK trypsin
time: 18 h
|
HBEs treated with 25ul of post trypsin media
25post18
|
| Sample_geo_accession | GSM528627
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528627/suppl/GSM528627_plate2_H01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528628 | GPL3921 |
|
HBEs treated with 25ul of post trypsin media 25post4_H6_1
|
Human bronchial epithelial cells (HBE)
|
final order: 90
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 25ul of post trypsin media
agent: post trypsin media
dose: 25ul 1 ug/ml TPCK trypsin
time: 4 h
|
HBEs treated with 25ul of post trypsin media
25post4
|
| Sample_geo_accession | GSM528628
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528628/suppl/GSM528628_plate1_H06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528629 | GPL3921 |
|
HBEs treated with 25ul of post trypsin media 25post8_D12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 144
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 25ul of post trypsin media
agent: post trypsin media
dose: 25ul 1 ug/ml TPCK trypsin
time: 8 h
|
HBEs treated with 25ul of post trypsin media
25post8
|
| Sample_geo_accession | GSM528629
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528629/suppl/GSM528629_plate2_D12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528630 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post0.5_C10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 34
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 0.5 h
|
HBEs treated with 500ul of post trypsin media
500post0.5
|
| Sample_geo_accession | GSM528630
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528630/suppl/GSM528630_plate1_C10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528631 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post0.5_C9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 33
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 0.5 h
|
HBEs treated with 500ul of post trypsin media
500post0.5
|
| Sample_geo_accession | GSM528631
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528631/suppl/GSM528631_plate1_C09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528632 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post1.5_F10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 70
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 1.5 h
|
HBEs treated with 500ul of post trypsin media
500post1.5
|
| Sample_geo_accession | GSM528632
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528632/suppl/GSM528632_plate1_F10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528633 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post1.5_F11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 71
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 1.5 h
|
HBEs treated with 500ul of post trypsin media
500post1.5
|
| Sample_geo_accession | GSM528633
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528633/suppl/GSM528633_plate1_F11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528634 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post18_H2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 182
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 18 h
|
HBEs treated with 500ul of post trypsin media
500post18
|
| Sample_geo_accession | GSM528634
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528634/suppl/GSM528634_plate2_H02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528635 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post18_H3_2
|
Human bronchial epithelial cells (HBE)
|
final order: 183
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 18 h
|
HBEs treated with 500ul of post trypsin media
500post18
|
| Sample_geo_accession | GSM528635
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528635/suppl/GSM528635_plate2_H03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528636 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post4_H7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 91
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 4 h
|
HBEs treated with 500ul of post trypsin media
500post4
|
| Sample_geo_accession | GSM528636
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528636/suppl/GSM528636_plate1_H07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528637 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post4_H8_2
|
Human bronchial epithelial cells (HBE)
|
final order: 92
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 4 h
|
HBEs treated with 500ul of post trypsin media
500post4
|
| Sample_geo_accession | GSM528637
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528637/suppl/GSM528637_plate1_H08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528638 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post8_E1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 145
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 8 h
|
HBEs treated with 500ul of post trypsin media
500post8
|
| Sample_geo_accession | GSM528638
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528638/suppl/GSM528638_plate2_E01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528639 | GPL3921 |
|
HBEs treated with 500ul of post trypsin media 500post8_E2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 146
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 500ul of post trypsin media
agent: post trypsin media
dose: 500ul 1 ug/ml TPCK trypsin
time: 8 h
|
HBEs treated with 500ul of post trypsin media
500post8
|
| Sample_geo_accession | GSM528639
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528639/suppl/GSM528639_plate2_E02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528640 | GPL3921 |
|
HBEs treated with 6ul of pre trypsin media 6pre0.5_C7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 31
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 6ul of pre trypsin media
agent: pre trypsin media
dose: 6ul 1 ug/ml TPCK trypsin
time: 0.5 h
|
HBEs treated with 6ul of pre trypsin media
6pre0.5
|
| Sample_geo_accession | GSM528640
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528640/suppl/GSM528640_plate1_C07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528641 | GPL3921 |
|
HBEs treated with 6ul of pre trypsin media 6pre1.5_F8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 68
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 6ul of pre trypsin media
agent: pre trypsin media
dose: 6ul 1 ug/ml TPCK trypsin
time: 1.5 h
|
HBEs treated with 6ul of pre trypsin media
6pre1.5
|
| Sample_geo_accession | GSM528641
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528641/suppl/GSM528641_plate1_F08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528642 | GPL3921 |
|
HBEs treated with 6ul of pre trypsin media 6pre18_G12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 180
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 6ul of pre trypsin media
agent: pre trypsin media
dose: 6ul 1 ug/ml TPCK trypsin
time: 18 h
|
HBEs treated with 6ul of pre trypsin media
6pre18
|
| Sample_geo_accession | GSM528642
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528642/suppl/GSM528642_plate2_G12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528643 | GPL3921 |
|
HBEs treated with 6ul of pre trypsin media 6pre4_H5_1
|
Human bronchial epithelial cells (HBE)
|
final order: 89
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 6ul of pre trypsin media
agent: pre trypsin media
dose: 6ul 1 ug/ml TPCK trypsin
time: 4 h
|
HBEs treated with 6ul of pre trypsin media
6pre4
|
| Sample_geo_accession | GSM528643
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528643/suppl/GSM528643_plate1_H05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528644 | GPL3921 |
|
HBEs treated with 6ul of pre trypsin media 6pre8_D11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 143
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with 6ul of pre trypsin media
agent: pre trypsin media
dose: 6ul 1 ug/ml TPCK trypsin
time: 8 h
|
HBEs treated with 6ul of pre trypsin media
6pre8
|
| Sample_geo_accession | GSM528644
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528644/suppl/GSM528644_plate2_D11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528645 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 94
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528645
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528645/suppl/GSM528645_plate1_H10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528646 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 95
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528646
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528646/suppl/GSM528646_plate1_H11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528647 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H12_3
|
Human bronchial epithelial cells (HBE)
|
final order: 96
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528647
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528647/suppl/GSM528647_plate1_H12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528648 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H5_4
|
Human bronchial epithelial cells (HBE)
|
final order: 185
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528648
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528648/suppl/GSM528648_plate2_H05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528649 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H6_5
|
Human bronchial epithelial cells (HBE)
|
final order: 186
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528649
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528649/suppl/GSM528649_plate2_H06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528650 | GPL3921 |
|
pooling of multiple samples to control for plate affects control-poolingAll_H7_6
|
Human bronchial epithelial cells (HBE)
|
final order: 187
cell type: Human bronchial epithelial cells (HBE)
sample type: pooling of multiple samples to control for plate affects
|
pooling of multiple samples to control for plate affects
control-poolingAll
|
| Sample_geo_accession | GSM528650
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528650/suppl/GSM528650_plate2_H07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528651 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post0.25_A11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 11
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 0.25 h
|
HBEs infected with delNS1 post trypsin
delNS1post0.25
|
| Sample_geo_accession | GSM528651
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528651/suppl/GSM528651_plate1_A11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528652 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post0.25_A12_2
|
Human bronchial epithelial cells (HBE)
|
final order: 12
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 0.25 h
|
HBEs infected with delNS1 post trypsin
delNS1post0.25
|
| Sample_geo_accession | GSM528652
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528652/suppl/GSM528652_plate1_A12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528653 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post0.5_C3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 27
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 0.5 h
|
HBEs infected with delNS1 post trypsin
delNS1post0.5
|
| Sample_geo_accession | GSM528653
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528653/suppl/GSM528653_plate1_C03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528654 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post0.5_C4_2
|
Human bronchial epithelial cells (HBE)
|
final order: 28
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 0.5 h
|
HBEs infected with delNS1 post trypsin
delNS1post0.5
|
| Sample_geo_accession | GSM528654
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528654/suppl/GSM528654_plate1_C04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528655 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post1.5_F4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 64
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 1.5 h
|
HBEs infected with delNS1 post trypsin
delNS1post1.5
|
| Sample_geo_accession | GSM528655
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528655/suppl/GSM528655_plate1_F04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528656 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post1.5_F5_2
|
Human bronchial epithelial cells (HBE)
|
final order: 65
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 1.5 h
|
HBEs infected with delNS1 post trypsin
delNS1post1.5
|
| Sample_geo_accession | GSM528656
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528656/suppl/GSM528656_plate1_F05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528657 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post1_D12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 48
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 1 h
|
HBEs infected with delNS1 post trypsin
delNS1post1
|
| Sample_geo_accession | GSM528657
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528657/suppl/GSM528657_plate1_D12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528658 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post1_E1_2
|
Human bronchial epithelial cells (HBE)
|
final order: 49
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 1 h
|
HBEs infected with delNS1 post trypsin
delNS1post1
|
| Sample_geo_accession | GSM528658
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528658/suppl/GSM528658_plate1_E01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528659 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post12_F4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 160
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 12 h
|
HBEs infected with delNS1 post trypsin
delNS1post12
|
| Sample_geo_accession | GSM528659
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528659/suppl/GSM528659_plate2_F04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528660 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post12_F5_2
|
Human bronchial epithelial cells (HBE)
|
final order: 161
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 12 h
|
HBEs infected with delNS1 post trypsin
delNS1post12
|
| Sample_geo_accession | GSM528660
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528660/suppl/GSM528660_plate2_F05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528661 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post18_G8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 176
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 18 h
|
HBEs infected with delNS1 post trypsin
delNS1post18
|
| Sample_geo_accession | GSM528661
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528661/suppl/GSM528661_plate2_G08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528662 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post18_G9_2
|
Human bronchial epithelial cells (HBE)
|
final order: 177
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 18 h
|
HBEs infected with delNS1 post trypsin
delNS1post18
|
| Sample_geo_accession | GSM528662
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528662/suppl/GSM528662_plate2_G09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528663 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post2_A11_a
|
Human bronchial epithelial cells (HBE)
|
final order: 107
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 2 h
|
HBEs infected with delNS1 post trypsin
delNS1post2
|
| Sample_geo_accession | GSM528663
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528663/suppl/GSM528663_plate2_A11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528664 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post2_A12_b
|
Human bronchial epithelial cells (HBE)
|
final order: 108
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 2 h
|
HBEs infected with delNS1 post trypsin
delNS1post2
|
| Sample_geo_accession | GSM528664
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528664/suppl/GSM528664_plate2_A12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528665 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post4_H1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 85
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 4 h
|
HBEs infected with delNS1 post trypsin
delNS1post4
|
| Sample_geo_accession | GSM528665
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528665/suppl/GSM528665_plate1_H01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528666 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post4_H2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 86
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 4 h
|
HBEs infected with delNS1 post trypsin
delNS1post4
|
| Sample_geo_accession | GSM528666
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528666/suppl/GSM528666_plate1_H02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528667 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post6_C3_a
|
Human bronchial epithelial cells (HBE)
|
final order: 123
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 6 h
|
HBEs infected with delNS1 post trypsin
delNS1post6
|
| Sample_geo_accession | GSM528667
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528667/suppl/GSM528667_plate2_C03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528668 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post6_C4_b
|
Human bronchial epithelial cells (HBE)
|
final order: 124
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 6 h
|
HBEs infected with delNS1 post trypsin
delNS1post6
|
| Sample_geo_accession | GSM528668
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528668/suppl/GSM528668_plate2_C04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528669 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post8_D7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 139
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 8 h
|
HBEs infected with delNS1 post trypsin
delNS1post8
|
| Sample_geo_accession | GSM528669
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528669/suppl/GSM528669_plate2_D07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528670 | GPL3921 |
|
HBEs infected with delNS1 post trypsin delNS1post8_D8_2
|
Human bronchial epithelial cells (HBE)
|
final order: 140
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 post trypsin
agent: delNS1 post trypsin
moi: 5
time: 8 h
|
HBEs infected with delNS1 post trypsin
delNS1post8
|
| Sample_geo_accession | GSM528670
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528670/suppl/GSM528670_plate2_D08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528671 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre0.25_A10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 10
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 0.25 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre0.25
|
| Sample_geo_accession | GSM528671
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528671/suppl/GSM528671_plate1_A10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528672 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre0.5_C2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 26
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 0.5 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre0.5
|
| Sample_geo_accession | GSM528672
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528672/suppl/GSM528672_plate1_C02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528673 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre1.5_F3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 63
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 1.5 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre1.5
|
| Sample_geo_accession | GSM528673
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528673/suppl/GSM528673_plate1_F03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528674 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre1_D11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 47
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 1 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre1
|
| Sample_geo_accession | GSM528674
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528674/suppl/GSM528674_plate1_D11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528675 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre12_F3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 159
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 12 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre12
|
| Sample_geo_accession | GSM528675
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528675/suppl/GSM528675_plate2_F03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528676 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre18_G7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 175
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 18 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre18
|
| Sample_geo_accession | GSM528676
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528676/suppl/GSM528676_plate2_G07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528677 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre2_A10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 106
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 2 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre2
|
| Sample_geo_accession | GSM528677
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528677/suppl/GSM528677_plate2_A10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528678 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre4_G12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 84
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 4 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre4
|
| Sample_geo_accession | GSM528678
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528678/suppl/GSM528678_plate1_G12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528679 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre6_C2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 122
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 6 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre6
|
| Sample_geo_accession | GSM528679
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528679/suppl/GSM528679_plate2_C02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528680 | GPL3921 |
|
HBEs infected with delNS1 pre trypsin delNS1pre8_D6_1
|
Human bronchial epithelial cells (HBE)
|
final order: 138
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with delNS1 pre trypsin
agent: delNS1 pre trypsin
moi: 5
time: 8 h
|
HBEs infected with delNS1 pre trypsin
delNS1pre8
|
| Sample_geo_accession | GSM528680
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528680/suppl/GSM528680_plate2_D06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528681 | GPL3921 |
|
HBEs treated with IFNb IFN0.25_B1_a
|
Human bronchial epithelial cells (HBE)
|
final order: 13
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 0.25 h
|
HBEs treated with IFNb
IFN0.25
|
| Sample_geo_accession | GSM528681
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528681/suppl/GSM528681_plate1_B01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528682 | GPL3921 |
|
HBEs treated with IFNb IFN0.25_B2_b
|
Human bronchial epithelial cells (HBE)
|
final order: 14
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 0.25 h
|
HBEs treated with IFNb
IFN0.25
|
| Sample_geo_accession | GSM528682
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528682/suppl/GSM528682_plate1_B02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528683 | GPL3921 |
|
HBEs treated with IFNb IFN0.5_C5_1
|
Human bronchial epithelial cells (HBE)
|
final order: 29
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 0.5 h
|
HBEs treated with IFNb
IFN0.5
|
| Sample_geo_accession | GSM528683
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528683/suppl/GSM528683_plate1_C05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528684 | GPL3921 |
|
HBEs treated with IFNb IFN0.5_C6_2
|
Human bronchial epithelial cells (HBE)
|
final order: 30
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 0.5 h
|
HBEs treated with IFNb
IFN0.5
|
| Sample_geo_accession | GSM528684
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528684/suppl/GSM528684_plate1_C06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528685 | GPL3921 |
|
HBEs treated with IFNb IFN1.5_F6_a
|
Human bronchial epithelial cells (HBE)
|
final order: 66
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 1.5 h
|
HBEs treated with IFNb
IFN1.5
|
| Sample_geo_accession | GSM528685
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528685/suppl/GSM528685_plate1_F06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528686 | GPL3921 |
|
HBEs treated with IFNb IFN1.5_F7_b
|
Human bronchial epithelial cells (HBE)
|
final order: 67
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 1.5 h
|
HBEs treated with IFNb
IFN1.5
|
| Sample_geo_accession | GSM528686
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528686/suppl/GSM528686_plate1_F07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528687 | GPL3921 |
|
HBEs treated with IFNb IFN1_E2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 50
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 1 h
|
HBEs treated with IFNb
IFN1
|
| Sample_geo_accession | GSM528687
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528687/suppl/GSM528687_plate1_E02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528688 | GPL3921 |
|
HBEs treated with IFNb IFN1_E3_2
|
Human bronchial epithelial cells (HBE)
|
final order: 51
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 1 h
|
HBEs treated with IFNb
IFN1
|
| Sample_geo_accession | GSM528688
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528688/suppl/GSM528688_plate1_E03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528689 | GPL3921 |
|
HBEs treated with IFNb IFN12_F6_1
|
Human bronchial epithelial cells (HBE)
|
final order: 162
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 12 h
|
HBEs treated with IFNb
IFN12
|
| Sample_geo_accession | GSM528689
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528689/suppl/GSM528689_plate2_F06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528690 | GPL3921 |
|
HBEs treated with IFNb IFN12_F7_2
|
Human bronchial epithelial cells (HBE)
|
final order: 163
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 12 h
|
HBEs treated with IFNb
IFN12
|
| Sample_geo_accession | GSM528690
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528690/suppl/GSM528690_plate2_F07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528691 | GPL3921 |
|
HBEs treated with IFNb IFN18_G10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 178
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 18 h
|
HBEs treated with IFNb
IFN18
|
| Sample_geo_accession | GSM528691
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528691/suppl/GSM528691_plate2_G10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528692 | GPL3921 |
|
HBEs treated with IFNb IFN18_G11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 179
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 18 h
|
HBEs treated with IFNb
IFN18
|
| Sample_geo_accession | GSM528692
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528692/suppl/GSM528692_plate2_G11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528693 | GPL3921 |
|
HBEs treated with IFNb IFN2_B1_a
|
Human bronchial epithelial cells (HBE)
|
final order: 109
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 2 h
|
HBEs treated with IFNb
IFN2
|
| Sample_geo_accession | GSM528693
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528693/suppl/GSM528693_plate2_B01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528694 | GPL3921 |
|
HBEs treated with IFNb IFN2_B2_b
|
Human bronchial epithelial cells (HBE)
|
final order: 110
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 2 h
|
HBEs treated with IFNb
IFN2
|
| Sample_geo_accession | GSM528694
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528694/suppl/GSM528694_plate2_B02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528695 | GPL3921 |
|
HBEs treated with IFNb IFN4_H3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 87
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 4 h
|
HBEs treated with IFNb
IFN4
|
| Sample_geo_accession | GSM528695
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528695/suppl/GSM528695_plate1_H03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528696 | GPL3921 |
|
HBEs treated with IFNb IFN4_H4_2
|
Human bronchial epithelial cells (HBE)
|
final order: 88
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 4 h
|
HBEs treated with IFNb
IFN4
|
| Sample_geo_accession | GSM528696
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528696/suppl/GSM528696_plate1_H04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528697 | GPL3921 |
|
HBEs treated with IFNb IFN6_C5_a
|
Human bronchial epithelial cells (HBE)
|
final order: 125
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 6 h
|
HBEs treated with IFNb
IFN6
|
| Sample_geo_accession | GSM528697
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528697/suppl/GSM528697_plate2_C05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528698 | GPL3921 |
|
HBEs treated with IFNb IFN6_C6_b
|
Human bronchial epithelial cells (HBE)
|
final order: 126
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 6 h
|
HBEs treated with IFNb
IFN6
|
| Sample_geo_accession | GSM528698
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528698/suppl/GSM528698_plate2_C06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528699 | GPL3921 |
|
HBEs treated with IFNb IFN8_D10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 142
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 8 h
|
HBEs treated with IFNb
IFN8
|
| Sample_geo_accession | GSM528699
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528699/suppl/GSM528699_plate2_D10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528700 | GPL3921 |
|
HBEs treated with IFNb IFN8_D9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 141
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with IFNb
agent: IFNb
dose: 1000 U/ml
time: 8 h
|
HBEs treated with IFNb
IFN8
|
| Sample_geo_accession | GSM528700
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528700/suppl/GSM528700_plate2_D09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528701 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA0.25_A3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 3
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 0.25 h
|
HBEs transfected with vRNA
LTX+RNA0.25
|
| Sample_geo_accession | GSM528701
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528701/suppl/GSM528701_plate1_A03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528702 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA0.25_A4_2
|
Human bronchial epithelial cells (HBE)
|
final order: 4
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 0.25 h
|
HBEs transfected with vRNA
LTX+RNA0.25
|
| Sample_geo_accession | GSM528702
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528702/suppl/GSM528702_plate1_A04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528703 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA0.5_B5_1
|
Human bronchial epithelial cells (HBE)
|
final order: 17
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 0.5 h
|
HBEs transfected with vRNA
LTX+RNA0.5
|
| Sample_geo_accession | GSM528703
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528703/suppl/GSM528703_plate1_B05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528704 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA0.5_B6_2
|
Human bronchial epithelial cells (HBE)
|
final order: 18
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 0.5 h
|
HBEs transfected with vRNA
LTX+RNA0.5
|
| Sample_geo_accession | GSM528704
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528704/suppl/GSM528704_plate1_B06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528705 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA1.5_E6_1
|
Human bronchial epithelial cells (HBE)
|
final order: 54
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 1.5 h
|
HBEs transfected with vRNA
LTX+RNA1.5
|
| Sample_geo_accession | GSM528705
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528705/suppl/GSM528705_plate1_E06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528706 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA1.5_E7_2
|
Human bronchial epithelial cells (HBE)
|
final order: 55
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 1.5 h
|
HBEs transfected with vRNA
LTX+RNA1.5
|
| Sample_geo_accession | GSM528706
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528706/suppl/GSM528706_plate1_E07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528707 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA1_D2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 38
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 1 h
|
HBEs transfected with vRNA
LTX+RNA1
|
| Sample_geo_accession | GSM528707
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528707/suppl/GSM528707_plate1_D02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528708 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA1_D3_2
|
Human bronchial epithelial cells (HBE)
|
final order: 39
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 1 h
|
HBEs transfected with vRNA
LTX+RNA1
|
| Sample_geo_accession | GSM528708
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528708/suppl/GSM528708_plate1_D03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528709 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA12_E6_1
|
Human bronchial epithelial cells (HBE)
|
final order: 150
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 12 h
|
HBEs transfected with vRNA
LTX+RNA12
|
| Sample_geo_accession | GSM528709
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528709/suppl/GSM528709_plate2_E06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528710 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA12_E7_2
|
Human bronchial epithelial cells (HBE)
|
final order: 151
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 12 h
|
HBEs transfected with vRNA
LTX+RNA12
|
| Sample_geo_accession | GSM528710
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528710/suppl/GSM528710_plate2_E07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528711 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA18_F10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 166
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 18 h
|
HBEs transfected with vRNA
LTX+RNA18
|
| Sample_geo_accession | GSM528711
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528711/suppl/GSM528711_plate2_F10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528712 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA18_F11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 167
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 18 h
|
HBEs transfected with vRNA
LTX+RNA18
|
| Sample_geo_accession | GSM528712
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528712/suppl/GSM528712_plate2_F11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528713 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA2_A1_a
|
Human bronchial epithelial cells (HBE)
|
final order: 97
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 2 h
|
HBEs transfected with vRNA
LTX+RNA2
|
| Sample_geo_accession | GSM528713
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528713/suppl/GSM528713_plate2_A01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528714 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA2_A2_b
|
Human bronchial epithelial cells (HBE)
|
final order: 98
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 2 h
|
HBEs transfected with vRNA
LTX+RNA2
|
| Sample_geo_accession | GSM528714
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528714/suppl/GSM528714_plate2_A02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528715 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA4_G3_a
|
Human bronchial epithelial cells (HBE)
|
final order: 75
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 4 h
|
HBEs transfected with vRNA
LTX+RNA4
|
| Sample_geo_accession | GSM528715
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528715/suppl/GSM528715_plate1_G03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528716 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA4_G4_b
|
Human bronchial epithelial cells (HBE)
|
final order: 76
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 4 h
|
HBEs transfected with vRNA
LTX+RNA4
|
| Sample_geo_accession | GSM528716
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528716/suppl/GSM528716_plate1_G04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528717 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA6_B5_a
|
Human bronchial epithelial cells (HBE)
|
final order: 113
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 6 h
|
HBEs transfected with vRNA
LTX+RNA6
|
| Sample_geo_accession | GSM528717
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528717/suppl/GSM528717_plate2_B05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528718 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA6_B6_b
|
Human bronchial epithelial cells (HBE)
|
final order: 114
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 6 h
|
HBEs transfected with vRNA
LTX+RNA6
|
| Sample_geo_accession | GSM528718
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528718/suppl/GSM528718_plate2_B06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528719 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA8_C10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 130
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 8 h
|
HBEs transfected with vRNA
LTX+RNA8
|
| Sample_geo_accession | GSM528719
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528719/suppl/GSM528719_plate2_C10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528720 | GPL3921 |
|
HBEs transfected with vRNA LTX+RNA8_C9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 129
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs transfected with vRNA
agent: vRNA
moi: 5
time: 8 h
|
HBEs transfected with vRNA
LTX+RNA8
|
| Sample_geo_accession | GSM528720
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528720/suppl/GSM528720_plate2_C09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528721 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX0.25_A1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 1
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 0.25 h
|
HBEs treated with LTX transfection reagent
LTX0.25
|
| Sample_geo_accession | GSM528721
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528721/suppl/GSM528721_plate1_A01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528722 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX0.25_A2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 2
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 0.25 h
|
HBEs treated with LTX transfection reagent
LTX0.25
|
| Sample_geo_accession | GSM528722
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528722/suppl/GSM528722_plate1_A02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528723 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX0.5_B3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 15
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 0.5 h
|
HBEs treated with LTX transfection reagent
LTX0.5
|
| Sample_geo_accession | GSM528723
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528723/suppl/GSM528723_plate1_B03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528724 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX0.5_B4_2
|
Human bronchial epithelial cells (HBE)
|
final order: 16
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 0.5 h
|
HBEs treated with LTX transfection reagent
LTX0.5
|
| Sample_geo_accession | GSM528724
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528724/suppl/GSM528724_plate1_B04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528725 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX1.5_E4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 52
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 1.5 h
|
HBEs treated with LTX transfection reagent
LTX1.5
|
| Sample_geo_accession | GSM528725
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528725/suppl/GSM528725_plate1_E04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528726 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX1.5_E5_2
|
Human bronchial epithelial cells (HBE)
|
final order: 53
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 1.5 h
|
HBEs treated with LTX transfection reagent
LTX1.5
|
| Sample_geo_accession | GSM528726
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528726/suppl/GSM528726_plate1_E05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528727 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX1_C12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 36
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 1 h
|
HBEs treated with LTX transfection reagent
LTX1
|
| Sample_geo_accession | GSM528727
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528727/suppl/GSM528727_plate1_C12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528728 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX1_D1_2
|
Human bronchial epithelial cells (HBE)
|
final order: 37
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 1 h
|
HBEs treated with LTX transfection reagent
LTX1
|
| Sample_geo_accession | GSM528728
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528728/suppl/GSM528728_plate1_D01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528729 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX12_E4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 148
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 12 h
|
HBEs treated with LTX transfection reagent
LTX12
|
| Sample_geo_accession | GSM528729
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528729/suppl/GSM528729_plate2_E04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528730 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX12_E5_2
|
Human bronchial epithelial cells (HBE)
|
final order: 149
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 12 h
|
HBEs treated with LTX transfection reagent
LTX12
|
| Sample_geo_accession | GSM528730
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528730/suppl/GSM528730_plate2_E05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528731 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX18_F8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 164
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 18 h
|
HBEs treated with LTX transfection reagent
LTX18
|
| Sample_geo_accession | GSM528731
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528731/suppl/GSM528731_plate2_F08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528732 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX18_F9_2
|
Human bronchial epithelial cells (HBE)
|
final order: 165
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 18 h
|
HBEs treated with LTX transfection reagent
LTX18
|
| Sample_geo_accession | GSM528732
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528732/suppl/GSM528732_plate2_F09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528733 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX4_G1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 73
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 4 h
|
HBEs treated with LTX transfection reagent
LTX4
|
| Sample_geo_accession | GSM528733
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528733/suppl/GSM528733_plate1_G01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528734 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX4_G2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 74
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 4 h
|
HBEs treated with LTX transfection reagent
LTX4
|
| Sample_geo_accession | GSM528734
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528734/suppl/GSM528734_plate1_G02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528735 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX6_B3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 111
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 6 h
|
HBEs treated with LTX transfection reagent
LTX6
|
| Sample_geo_accession | GSM528735
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528735/suppl/GSM528735_plate2_B03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528736 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX6_B4_2
|
Human bronchial epithelial cells (HBE)
|
final order: 112
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 6 h
|
HBEs treated with LTX transfection reagent
LTX6
|
| Sample_geo_accession | GSM528736
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528736/suppl/GSM528736_plate2_B04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528737 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX8_C7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 127
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 8 h
|
HBEs treated with LTX transfection reagent
LTX8
|
| Sample_geo_accession | GSM528737
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528737/suppl/GSM528737_plate2_C07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528738 | GPL3921 |
|
HBEs treated with LTX transfection reagent LTX8_C8_2
|
Human bronchial epithelial cells (HBE)
|
final order: 128
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with LTX transfection reagent
agent: LTX transfection reagent
time: 8 h
|
HBEs treated with LTX transfection reagent
LTX8
|
| Sample_geo_accession | GSM528738
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528738/suppl/GSM528738_plate2_C08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528739 | GPL3921 |
|
HBEs treated with media alone MockIFN0.25_A7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 7
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 0.25 h
|
HBEs treated with media alone
MockIFN0.25
|
| Sample_geo_accession | GSM528739
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528739/suppl/GSM528739_plate1_A07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528740 | GPL3921 |
|
HBEs treated with media alone MockIFN0.25_A8_2
|
Human bronchial epithelial cells (HBE)
|
final order: 8
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 0.25 h
|
HBEs treated with media alone
MockIFN0.25
|
| Sample_geo_accession | GSM528740
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528740/suppl/GSM528740_plate1_A08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528741 | GPL3921 |
|
HBEs treated with media alone MockIFN0.5_B10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 22
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 0.5 h
|
HBEs treated with media alone
MockIFN0.5
|
| Sample_geo_accession | GSM528741
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528741/suppl/GSM528741_plate1_B10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528742 | GPL3921 |
|
HBEs treated with media alone MockIFN0.5_B9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 21
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 0.5 h
|
HBEs treated with media alone
MockIFN0.5
|
| Sample_geo_accession | GSM528742
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528742/suppl/GSM528742_plate1_B09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528743 | GPL3921 |
|
HBEs treated with media alone MockIFN1.5_E10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 58
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 1.5 h
|
HBEs treated with media alone
MockIFN1.5
|
| Sample_geo_accession | GSM528743
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528743/suppl/GSM528743_plate1_E10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528744 | GPL3921 |
|
HBEs treated with media alone MockIFN1.5_E11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 59
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 1.5 h
|
HBEs treated with media alone
MockIFN1.5
|
| Sample_geo_accession | GSM528744
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528744/suppl/GSM528744_plate1_E11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528745 | GPL3921 |
|
HBEs treated with media alone MockIFN1_D6_a
|
Human bronchial epithelial cells (HBE)
|
final order: 42
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 1 h
|
HBEs treated with media alone
MockIFN1
|
| Sample_geo_accession | GSM528745
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528745/suppl/GSM528745_plate1_D06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528746 | GPL3921 |
|
HBEs treated with media alone MockIFN1_D7_b
|
Human bronchial epithelial cells (HBE)
|
final order: 43
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 1 h
|
HBEs treated with media alone
MockIFN1
|
| Sample_geo_accession | GSM528746
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528746/suppl/GSM528746_plate1_D07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528747 | GPL3921 |
|
HBEs treated with media alone MockIFN12_E10_1
|
Human bronchial epithelial cells (HBE)
|
final order: 154
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 12 h
|
HBEs treated with media alone
MockIFN12
|
| Sample_geo_accession | GSM528747
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528747/suppl/GSM528747_plate2_E10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528748 | GPL3921 |
|
HBEs treated with media alone MockIFN12_E11_2
|
Human bronchial epithelial cells (HBE)
|
final order: 155
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 12 h
|
HBEs treated with media alone
MockIFN12
|
| Sample_geo_accession | GSM528748
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528748/suppl/GSM528748_plate2_E11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528749 | GPL3921 |
|
HBEs treated with media alone MockIFN18_G2_1
|
Human bronchial epithelial cells (HBE)
|
final order: 170
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 18 h
|
HBEs treated with media alone
MockIFN18
|
| Sample_geo_accession | GSM528749
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528749/suppl/GSM528749_plate2_G02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528750 | GPL3921 |
|
HBEs treated with media alone MockIFN18_G3_2
|
Human bronchial epithelial cells (HBE)
|
final order: 171
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 18 h
|
HBEs treated with media alone
MockIFN18
|
| Sample_geo_accession | GSM528750
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528750/suppl/GSM528750_plate2_G03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528751 | GPL3921 |
|
HBEs treated with media alone MockIFN2_A5_a
|
Human bronchial epithelial cells (HBE)
|
final order: 101
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 2 h
|
HBEs treated with media alone
MockIFN2
|
| Sample_geo_accession | GSM528751
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528751/suppl/GSM528751_plate2_A05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528752 | GPL3921 |
|
HBEs treated with media alone MockIFN2_A6_b
|
Human bronchial epithelial cells (HBE)
|
final order: 102
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 2 h
|
HBEs treated with media alone
MockIFN2
|
| Sample_geo_accession | GSM528752
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528752/suppl/GSM528752_plate2_A06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528753 | GPL3921 |
|
HBEs treated with media alone MockIFN4_G7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 79
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 4 h
|
HBEs treated with media alone
MockIFN4
|
| Sample_geo_accession | GSM528753
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528753/suppl/GSM528753_plate1_G07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528754 | GPL3921 |
|
HBEs treated with media alone MockIFN4_G8_2
|
Human bronchial epithelial cells (HBE)
|
final order: 80
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 4 h
|
HBEs treated with media alone
MockIFN4
|
| Sample_geo_accession | GSM528754
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528754/suppl/GSM528754_plate1_G08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528755 | GPL3921 |
|
HBEs treated with media alone MockIFN6_B10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 118
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 6 h
|
HBEs treated with media alone
MockIFN6
|
| Sample_geo_accession | GSM528755
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528755/suppl/GSM528755_plate2_B10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528756 | GPL3921 |
|
HBEs treated with media alone MockIFN6_B9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 117
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 6 h
|
HBEs treated with media alone
MockIFN6
|
| Sample_geo_accession | GSM528756
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528756/suppl/GSM528756_plate2_B09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528757 | GPL3921 |
|
HBEs treated with media alone MockIFN8_D1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 133
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 8 h
|
HBEs treated with media alone
MockIFN8
|
| Sample_geo_accession | GSM528757
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528757/suppl/GSM528757_plate2_D01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528758 | GPL3921 |
|
HBEs treated with media alone MockIFN8_D2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 134
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs treated with media alone
agent: media alone
time: 8 h
|
HBEs treated with media alone
MockIFN8
|
| Sample_geo_accession | GSM528758
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528758/suppl/GSM528758_plate2_D02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528759 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post0.25_H8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 188
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 0.25 h
|
HBEs infected with PR8 post trypsin
PR8post0.25
|
| Sample_geo_accession | GSM528759
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528759/suppl/GSM528759_plate2_H08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528760 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post0.25_H9_2
|
Human bronchial epithelial cells (HBE)
|
final order: 189
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 0.25 h
|
HBEs infected with PR8 post trypsin
PR8post0.25
|
| Sample_geo_accession | GSM528760
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528760/suppl/GSM528760_plate2_H09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528761 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post0.5_B12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 24
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 0.5 h
|
HBEs infected with PR8 post trypsin
PR8post0.5
|
| Sample_geo_accession | GSM528761
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528761/suppl/GSM528761_plate1_B12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528762 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post0.5_C1_2
|
Human bronchial epithelial cells (HBE)
|
final order: 25
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 0.5 h
|
HBEs infected with PR8 post trypsin
PR8post0.5
|
| Sample_geo_accession | GSM528762
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528762/suppl/GSM528762_plate1_C01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528763 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post1.5_F1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 61
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 1.5 h
|
HBEs infected with PR8 post trypsin
PR8post1.5
|
| Sample_geo_accession | GSM528763
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528763/suppl/GSM528763_plate1_F01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528764 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post1.5_F2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 62
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 1.5 h
|
HBEs infected with PR8 post trypsin
PR8post1.5
|
| Sample_geo_accession | GSM528764
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528764/suppl/GSM528764_plate1_F02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528765 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post1_D10_2
|
Human bronchial epithelial cells (HBE)
|
final order: 46
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 1 h
|
HBEs infected with PR8 post trypsin
PR8post1
|
| Sample_geo_accession | GSM528765
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528765/suppl/GSM528765_plate1_D10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528766 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post1_D9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 45
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 1 h
|
HBEs infected with PR8 post trypsin
PR8post1
|
| Sample_geo_accession | GSM528766
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528766/suppl/GSM528766_plate1_D09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528767 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post12_F1_1
|
Human bronchial epithelial cells (HBE)
|
final order: 157
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 12 h
|
HBEs infected with PR8 post trypsin
PR8post12
|
| Sample_geo_accession | GSM528767
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528767/suppl/GSM528767_plate2_F01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528768 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post12_F2_2
|
Human bronchial epithelial cells (HBE)
|
final order: 158
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 12 h
|
HBEs infected with PR8 post trypsin
PR8post12
|
| Sample_geo_accession | GSM528768
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528768/suppl/GSM528768_plate2_F02.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528769 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post18_G5_1
|
Human bronchial epithelial cells (HBE)
|
final order: 173
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 18 h
|
HBEs infected with PR8 post trypsin
PR8post18
|
| Sample_geo_accession | GSM528769
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528769/suppl/GSM528769_plate2_G05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528770 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post18_G6_2
|
Human bronchial epithelial cells (HBE)
|
final order: 174
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 18 h
|
HBEs infected with PR8 post trypsin
PR8post18
|
| Sample_geo_accession | GSM528770
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528770/suppl/GSM528770_plate2_G06.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528771 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post2_A8_a
|
Human bronchial epithelial cells (HBE)
|
final order: 104
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 2 h
|
HBEs infected with PR8 post trypsin
PR8post2
|
| Sample_geo_accession | GSM528771
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528771/suppl/GSM528771_plate2_A08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528772 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post2_A9_b
|
Human bronchial epithelial cells (HBE)
|
final order: 105
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 2 h
|
HBEs infected with PR8 post trypsin
PR8post2
|
| Sample_geo_accession | GSM528772
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528772/suppl/GSM528772_plate2_A09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528773 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post4_G10_a
|
Human bronchial epithelial cells (HBE)
|
final order: 82
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 4 h
|
HBEs infected with PR8 post trypsin
PR8post4
|
| Sample_geo_accession | GSM528773
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528773/suppl/GSM528773_plate1_G10.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528774 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post4_G11_b
|
Human bronchial epithelial cells (HBE)
|
final order: 83
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 4 h
|
HBEs infected with PR8 post trypsin
PR8post4
|
| Sample_geo_accession | GSM528774
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528774/suppl/GSM528774_plate1_G11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528775 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post6_B12_a
|
Human bronchial epithelial cells (HBE)
|
final order: 120
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 6 h
|
HBEs infected with PR8 post trypsin
PR8post6
|
| Sample_geo_accession | GSM528775
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528775/suppl/GSM528775_plate2_B12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528776 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post6_C1_b
|
Human bronchial epithelial cells (HBE)
|
final order: 121
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 6 h
|
HBEs infected with PR8 post trypsin
PR8post6
|
| Sample_geo_accession | GSM528776
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528776/suppl/GSM528776_plate2_C01.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528777 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post8_D4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 136
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 8 h
|
HBEs infected with PR8 post trypsin
PR8post8
|
| Sample_geo_accession | GSM528777
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528777/suppl/GSM528777_plate2_D04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528778 | GPL3921 |
|
HBEs infected with PR8 post trypsin PR8post8_D5_2
|
Human bronchial epithelial cells (HBE)
|
final order: 137
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 post trypsin
agent: PR8 post trypsin
moi: 5
time: 8 h
|
HBEs infected with PR8 post trypsin
PR8post8
|
| Sample_geo_accession | GSM528778
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528778/suppl/GSM528778_plate2_D05.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528779 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre0.25_A9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 9
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 0.25 h
|
HBEs infected with PR8 pre trypsin
PR8pre0.25
|
| Sample_geo_accession | GSM528779
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528779/suppl/GSM528779_plate1_A09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528780 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre0.5_B11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 23
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 0.5 h
|
HBEs infected with PR8 pre trypsin
PR8pre0.5
|
| Sample_geo_accession | GSM528780
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528780/suppl/GSM528780_plate1_B11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528781 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre1.5_E12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 60
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 1.5 h
|
HBEs infected with PR8 pre trypsin
PR8pre1.5
|
| Sample_geo_accession | GSM528781
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528781/suppl/GSM528781_plate1_E12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528782 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre1_D8_1
|
Human bronchial epithelial cells (HBE)
|
final order: 44
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 1 h
|
HBEs infected with PR8 pre trypsin
PR8pre1
|
| Sample_geo_accession | GSM528782
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528782/suppl/GSM528782_plate1_D08.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528783 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre12_E12_1
|
Human bronchial epithelial cells (HBE)
|
final order: 156
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 12 h
|
HBEs infected with PR8 pre trypsin
PR8pre12
|
| Sample_geo_accession | GSM528783
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528783/suppl/GSM528783_plate2_E12.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528784 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre18_G4_1
|
Human bronchial epithelial cells (HBE)
|
final order: 172
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 18 h
|
HBEs infected with PR8 pre trypsin
PR8pre18
|
| Sample_geo_accession | GSM528784
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528784/suppl/GSM528784_plate2_G04.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528785 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre2_A7_1
|
Human bronchial epithelial cells (HBE)
|
final order: 103
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 2 h
|
HBEs infected with PR8 pre trypsin
PR8pre2
|
| Sample_geo_accession | GSM528785
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528785/suppl/GSM528785_plate2_A07.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528786 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre4_G9_1
|
Human bronchial epithelial cells (HBE)
|
final order: 81
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 4 h
|
HBEs infected with PR8 pre trypsin
PR8pre4
|
| Sample_geo_accession | GSM528786
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528786/suppl/GSM528786_plate1_G09.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528787 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre6_B11_1
|
Human bronchial epithelial cells (HBE)
|
final order: 119
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 6 h
|
HBEs infected with PR8 pre trypsin
PR8pre6
|
| Sample_geo_accession | GSM528787
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528787/suppl/GSM528787_plate2_B11.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
|
GSM528788 | GPL3921 |
|
HBEs infected with PR8 pre trypsin PR8pre8_D3_1
|
Human bronchial epithelial cells (HBE)
|
final order: 135
cell type: Human bronchial epithelial cells (HBE)
sample type: HBEs infected with PR8 pre trypsin
agent: PR8 pre trypsin
moi: 5
time: 8 h
|
HBEs infected with PR8 pre trypsin
PR8pre8
|
| Sample_geo_accession | GSM528788
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Mar 30 2010
| | Sample_last_update_date | Apr 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HBECs were stimulated with a 15 minute pulse of 1000U/ml IFNβ (PBL, Piscataway, NJ), 100ng/ml vRNA (purified directly from PR8 virus) with LTX transfection reagent (Invitrogen; Carlsbad, California), wild type H1N1 influenza (A/PR/8/34) or ΔNS1 virus (PR8 with a deleted NS1 gene, gift from Dr. Garcia-Sastre). Viruses were used at a multiplicity of infection (moi) of 5. Control samples were incubated with media or LTX under the same conditions. Cells were washed, supplemented with warm media and harvested at 11 timepoints (0, .25, .5, 1, 1.5, 2, 4, 6, 8, 12, and 18 hours post-treatment). HBECs were seeded in 6 well plates at a concentration of 250,000/well 18 hours prior to stimultaion. Cells were stimulated with a 15 minute pulse of IFNb, vRNA, infected with PR8 influenza or NS1 deleted influenza, or mock treated. In order to concentrate virus, red blood cells were used to bind virus for 30 minutes. Trypsin was then used to detach virus form the red blood cells. This was then spun at 1200 RPM for 5 minutes to separate RBCs from virus. The resulting supernatant was used to infect cells. As a control, we also made supernatant from RBCs that underwhent the same process but in the abcence of virus and used different ammount to treat cells for various times; these samples are included in this submission and are designated as pre (for pre trypsin) and post (for post trypsin). Analysis shows that there was no difference between these treatments and media alone.
| | Sample_growth_protocol_ch1 | HBECs were maintained in bronchial epithelial cell basal medium (Lonza) containing hrEGF (25 ng/ml), bovine pituitary extract (65 ng/ml), 50 nM all trans-retinoic acid, BSA (1.5 μg/ml), nystatin (20 IU/ml; GIBCO), hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), transferrin (10 μg/ml), epinephrine (0.5 μg/ml), triiodothyronine (6.5 ng/ml), gentamicin (50 μg/ml), and 50 μg/ml amphotericin-B (Cambrex).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling Assay, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A HT Arrays. HT Arrays were washed and stained on the GeneChip Array Station
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix High Throughput Array Plate Scanner
| | Sample_data_processing | Data (in matrix) were normalized using RMA. Probes that were lower than 20 in all samples were removed and all values less than 20 were replaced by 20 for all remaining probes
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Nir,,Hacohen
| | Sample_contact_email | nhacohen@partners.org
| | Sample_contact_phone | 617-724-3768
| | Sample_contact_institute | Broad Institute
| | Sample_contact_address | 7 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02129
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528788/suppl/GSM528788_plate2_D03.CEL.gz
| | Sample_series_id | GSE19392
| | Sample_data_row_count | 22277
| | |
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