Search results for the GEO ID: GSE13396  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM344588 | GPL201 |
|
mock-infected, normal S1 (HG-Focus array)
|
mock-infected PBE cells, normal S01, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344588
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344588/suppl/GSM344588.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344589 | GPL201 |
|
mock-infected, normal S2 (HG-Focus array)
|
mock-infected PBE cells, normal S02, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344589
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344589/suppl/GSM344589.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344590 | GPL201 |
|
mock-infected, normal S3 (HG-Focus array)
|
mock-infected PBE cells, normal S03, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344590
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344590/suppl/GSM344590.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344591 | GPL201 |
|
HRV-infected, normal S1 (HG-Focus array)
|
HRV-infected PBE cells, normal S01, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344591
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344591/suppl/GSM344591.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344592 | GPL201 |
|
HRV-infected, normal S2 (HG-Focus array)
|
HRV-infected PBE cells, normal S02, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344592
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344592/suppl/GSM344592.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344593 | GPL201 |
|
HRV-infected, normal S3 (HG-Focus array)
|
HRV-infected PBE cells, normal S03, 16 h p.i.
|
Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from normal (control) individual
|
| Sample_geo_accession | GSM344593
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344593/suppl/GSM344593.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344594 | GPL201 |
|
mock-infected, asthmatic S4 (HG-Focus array)
|
mock-infected PBE cells, asthmatic S04, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344594
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344594/suppl/GSM344594.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344595 | GPL201 |
|
mock-infected, asthmatic S5 (HG-Focus array)
|
mock-infected PBE cells, asthmatic S05, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344595
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344595/suppl/GSM344595.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344596 | GPL201 |
|
mock-infected, asthmatic S6 (HG-Focus array)
|
mock-infected PBE cells, asthmatic S06, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from mock-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344596
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344596/suppl/GSM344596.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344597 | GPL201 |
|
HRV-infected, asthmatic S4 (HG-Focus array)
|
HRV-infected PBE cells, asthmatic S04, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344597
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344597/suppl/GSM344597.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344598 | GPL201 |
|
HRV-infected, asthmatic S5 (HG-Focus array)
|
HRV-infected PBE cells, asthmatic S05, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344598
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344598/suppl/GSM344598.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
|
GSM344599 | GPL201 |
|
HRV-infected, asthmatic S6 (HG-Focus array)
|
HRV-infected PBE cells, asthmatic S06, 16 h p.i.
|
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
|
Gene expression data from HRV-infected PBE cells from asthmatic individual
|
| Sample_geo_accession | GSM344599
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | Nov 21 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
| | Sample_growth_protocol_ch1 | Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human HG-Focus Focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the HP GeneArray Scanner (Hewlett-Packard).
| | Sample_data_processing | Fluorescent signal intensities were extracted from scanned images by Affymetrix Microarray Suite 5.0 software using their statistical expression algorithm. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. Log2 transformed expression values across all the chips were obtained using the Robust Multichip Average (RMA) method with median scaling as normalization.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Yury,A,Bochkov
| | Sample_contact_email | yabochkov@wisc.edu
| | Sample_contact_phone | 608-263-8553
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University Of Wisconsin-Madison
| | Sample_contact_address | 600 Highland Ave, K4/945 CSC
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53792-9988
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344599/suppl/GSM344599.CEL.gz
| | Sample_series_id | GSE13396
| | Sample_data_row_count | 8793
| | |
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