Search results for the GEO ID: GSE10718  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM270872 | GPL570 |
|
Mock 1h repA
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 1h repA
|
| Sample_geo_accession | GSM270872
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270872/suppl/GSM270872.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270872/suppl/GSM270872.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270873 | GPL570 |
|
Mock 1h repB
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 1h repB
|
| Sample_geo_accession | GSM270873
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270873/suppl/GSM270873.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270873/suppl/GSM270873.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270874 | GPL570 |
|
Mock 1h repC
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 1h repC
|
| Sample_geo_accession | GSM270874
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270874/suppl/GSM270874.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270874/suppl/GSM270874.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270875 | GPL570 |
|
Mock 2h repA
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 2h repA
|
| Sample_geo_accession | GSM270875
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270875/suppl/GSM270875.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270875/suppl/GSM270875.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270876 | GPL570 |
|
Mock 2h repB
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 2h repB
|
| Sample_geo_accession | GSM270876
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270876/suppl/GSM270876.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270876/suppl/GSM270876.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270878 | GPL570 |
|
Mock 2h repC
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 2h repC
|
| Sample_geo_accession | GSM270878
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270878/suppl/GSM270878.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270878/suppl/GSM270878.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270879 | GPL570 |
|
Mock 4h repA
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 4h repA
|
| Sample_geo_accession | GSM270879
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270879/suppl/GSM270879.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270879/suppl/GSM270879.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270880 | GPL570 |
|
Mock 4h repB
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 4h repB
|
| Sample_geo_accession | GSM270880
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270880/suppl/GSM270880.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270880/suppl/GSM270880.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270881 | GPL570 |
|
Mock 4h repC
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 4h repC
|
| Sample_geo_accession | GSM270881
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270881/suppl/GSM270881.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270881/suppl/GSM270881.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270882 | GPL570 |
|
Mock 24h repA
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 24h repA
|
| Sample_geo_accession | GSM270882
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270882/suppl/GSM270882.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270882/suppl/GSM270882.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270883 | GPL570 |
|
Mock 24h repB
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 24h repB
|
| Sample_geo_accession | GSM270883
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270883/suppl/GSM270883.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270883/suppl/GSM270883.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270884 | GPL570 |
|
Mock 24h repC
|
mock exposed NHBE cells
|
NHBE cells
|
Mock 24h repC
|
| Sample_geo_accession | GSM270884
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270884/suppl/GSM270884.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270884/suppl/GSM270884.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270885 | GPL570 |
|
Smoke 1h repA
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 1h repA
|
| Sample_geo_accession | GSM270885
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270885/suppl/GSM270885.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270885/suppl/GSM270885.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270886 | GPL570 |
|
Smoke 1h repB
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 1h repB
|
| Sample_geo_accession | GSM270886
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270886/suppl/GSM270886.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270886/suppl/GSM270886.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270887 | GPL570 |
|
Smoke 1h repC
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 1h repC
|
| Sample_geo_accession | GSM270887
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270887/suppl/GSM270887.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270887/suppl/GSM270887.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270888 | GPL570 |
|
Smoke 2h repA
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 2h repA
|
| Sample_geo_accession | GSM270888
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270888/suppl/GSM270888.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270888/suppl/GSM270888.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270889 | GPL570 |
|
Smoke 2h repB
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 2h repB
|
| Sample_geo_accession | GSM270889
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270889/suppl/GSM270889.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270889/suppl/GSM270889.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270890 | GPL570 |
|
Smoke 2h repC
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 2h repC
|
| Sample_geo_accession | GSM270890
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270890/suppl/GSM270890.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270890/suppl/GSM270890.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270891 | GPL570 |
|
Smoke 4h repA
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 4h repA
|
| Sample_geo_accession | GSM270891
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270891/suppl/GSM270891.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270891/suppl/GSM270891.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270892 | GPL570 |
|
Smoke 4h repB
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 4h repB
|
| Sample_geo_accession | GSM270892
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270892/suppl/GSM270892.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270892/suppl/GSM270892.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270893 | GPL570 |
|
Smoke 4h repC
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 4h repC
|
| Sample_geo_accession | GSM270893
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270893/suppl/GSM270893.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270893/suppl/GSM270893.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270894 | GPL570 |
|
Smoke 24h repA
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 24h repA
|
| Sample_geo_accession | GSM270894
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270894/suppl/GSM270894.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270894/suppl/GSM270894.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270895 | GPL570 |
|
Smoke 24h repB
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 24h repB
|
| Sample_geo_accession | GSM270895
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270895/suppl/GSM270895.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270895/suppl/GSM270895.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
GSM270896 | GPL570 |
|
Smoke 24h repC
|
smoke exposed NHBE cells
|
NHBE cells
|
Smoke 24h repC
|
| Sample_geo_accession | GSM270896
| | Sample_status | Public on Mar 05 2008
| | Sample_submission_date | Mar 04 2008
| | Sample_last_update_date | Mar 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS. Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled). The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure. The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke. Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)
| | Sample_growth_protocol_ch1 | NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD). Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix
| | Sample_hyb_protocol | Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450
| | Sample_scan_protocol | Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).
| | Sample_data_processing | MAS5 algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ellen,,Jorgensen
| | Sample_contact_email | ejorgensen@vectorgroupltd.com
| | Sample_contact_institute | Vector Research Ltd.
| | Sample_contact_address | 712 Fifth Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10019
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270896/suppl/GSM270896.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270896/suppl/GSM270896.CHP.gz
| | Sample_series_id | GSE10718
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
