Search results for the GEO ID: GSE46914  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1141035 | GPL570 |
|
PBMCs_HV2_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141035
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141035/suppl/GSM1141035_HV2-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141036 | GPL570 |
|
PBMCs_HV2_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141036
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141036/suppl/GSM1141036_HV2-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141037 | GPL570 |
|
PBMCs_HV2_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141037
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141037/suppl/GSM1141037_HV2-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141038 | GPL570 |
|
PBMCs_HV2_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141038
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141038/suppl/GSM1141038_HV2-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141039 | GPL570 |
|
PBMCs_HV3_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141039
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141039/suppl/GSM1141039_HV3-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141040 | GPL570 |
|
PBMCs_HV3_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141040
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141040/suppl/GSM1141040_HV3-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141041 | GPL570 |
|
PBMCs_HV3_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141041
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141041/suppl/GSM1141041_HV3-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141042 | GPL570 |
|
PBMCs_HV3_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141042
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141042/suppl/GSM1141042_HV3-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141043 | GPL570 |
|
PBMCs_HV5_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141043
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141043/suppl/GSM1141043_HV5-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141044 | GPL570 |
|
PBMCs_HV5_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141044
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141044/suppl/GSM1141044_HV5-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141045 | GPL570 |
|
PBMCs_HV5_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141045
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141045/suppl/GSM1141045_HV5-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141046 | GPL570 |
|
PBMCs_HV5_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141046
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141046/suppl/GSM1141046_HV5-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141047 | GPL570 |
|
PBMCs_HV6_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141047
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141047/suppl/GSM1141047_HV6-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141048 | GPL570 |
|
PBMCs_HV6_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141048
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141048/suppl/GSM1141048_HV6-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141049 | GPL570 |
|
PBMCs_HV6_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141049
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141049/suppl/GSM1141049_HV6-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141050 | GPL570 |
|
PBMCs_HV6_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141050
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141050/suppl/GSM1141050_HV6-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141051 | GPL570 |
|
PBMCs_HV7_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141051
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141051/suppl/GSM1141051_HV7-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141052 | GPL570 |
|
PBMCs_HV7_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141052
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141052/suppl/GSM1141052_HV7-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141053 | GPL570 |
|
PBMCs_HV7_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141053
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141053/suppl/GSM1141053_HV7-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141054 | GPL570 |
|
PBMCs_HV7_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141054
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141054/suppl/GSM1141054_HV7-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141055 | GPL570 |
|
PBMCs_HV9_medium
|
PBMCs
|
culture condition: medium
|
|
| Sample_geo_accession | GSM1141055
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141055/suppl/GSM1141055_HV9-1.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141056 | GPL570 |
|
PBMCs_HV9_LPS unprimed
|
PBMCs
|
culture condition: LPS unprimed
|
|
| Sample_geo_accession | GSM1141056
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141056/suppl/GSM1141056_HV9-2.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141057 | GPL570 |
|
PBMCs_HV9_LPS primed
|
PBMCs
|
culture condition: LPS primed
|
|
| Sample_geo_accession | GSM1141057
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141057/suppl/GSM1141057_HV9-3.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
GSM1141058 | GPL570 |
|
PBMCs_HV9_LPS primed+IFNg
|
PBMCs
|
culture condition: LPS primed + IFNg
|
|
| Sample_geo_accession | GSM1141058
| | Sample_status | Public on Jul 31 2013
| | Sample_submission_date | May 14 2013
| | Sample_last_update_date | Jul 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Genechip scanner 3000.
| | Sample_data_processing | Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Florence,,Frager
| | Sample_contact_email | florence.frager@hotmail.com
| | Sample_contact_laboratory | pavillon P 5eme etage
| | Sample_contact_department | LCR HCL-biomérieux
| | Sample_contact_institute | biomerieux
| | Sample_contact_address | 5 place d'arsonval
| | Sample_contact_city | Lyon
| | Sample_contact_zip/postal_code | 69003
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1141nnn/GSM1141058/suppl/GSM1141058_HV9-4.CEL.gz
| | Sample_series_id | GSE46914
| | Sample_data_row_count | 54675
| | |
|
| |
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