Search results for the GEO ID: GSE14385  |
(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 |
GSM359557 | GPL570 |
|
csc-aza-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: csc
Demethylation: aza
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359557
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359557/suppl/GSM359557.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359558 | GPL570 |
|
csc-aza-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: csc
Demethylation: aza
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359558
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359558/suppl/GSM359558.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359559 | GPL570 |
|
dmso-none-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: none
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359559
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359559/suppl/GSM359559.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359560 | GPL570 |
|
dmso-aza-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: aza
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359560
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359560/suppl/GSM359560.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359561 | GPL570 |
|
untreated-none-3
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: none
Replicate: 3
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359561
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359561/suppl/GSM359561.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359562 | GPL570 |
|
dmso-none-3
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: none
Replicate: 3
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359562
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359562/suppl/GSM359562.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359563 | GPL570 |
|
untreated-aza-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: aza
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359563
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359563/suppl/GSM359563.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359564 | GPL570 |
|
untreated-none-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: none
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359564
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359564/suppl/GSM359564.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359565 | GPL570 |
|
dmso-aza-3
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: aza
Replicate: 3
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359565
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359565/suppl/GSM359565.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359566 | GPL570 |
|
csc-none-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: csc
Demethylation: none
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359566
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359566/suppl/GSM359566.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359567 | GPL570 |
|
csc-none-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: csc
Demethylation: none
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359567
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359567/suppl/GSM359567.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359568 | GPL570 |
|
untreated-aza-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: aza
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359568
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359568/suppl/GSM359568.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359569 | GPL570 |
|
dmso-none-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: none
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359569
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359569/suppl/GSM359569.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359570 | GPL570 |
|
untreated-aza-3
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: aza
Replicate: 3
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359570
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359570/suppl/GSM359570.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359571 | GPL570 |
|
untreated-none-2
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: untreated
Demethylation: none
Replicate: 2
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359571
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359571/suppl/GSM359571.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359572 | GPL570 |
|
csc-none-3
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: none
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: csc
Demethylation: none
Replicate: 3
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359572
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359572/suppl/GSM359572.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
GSM359573 | GPL570 |
|
dmso-aza-1
|
normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: aza
|
normal human bronchial epithelial cells (BEAS-2B)
Treatment: dmso
Demethylation: aza
Replicate: 1
|
Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent
|
| Sample_geo_accession | GSM359573
| | Sample_status | Public on Aug 01 2009
| | Sample_submission_date | Jan 12 2009
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.
| | Sample_growth_protocol_ch1 | BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.
| | Sample_hyb_protocol | 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).
| | Sample_scan_protocol | Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hubert,,Rehrauer
| | Sample_contact_email | Hubert.Rehrauer@fgcz.ethz.ch
| | Sample_contact_institute | FGCZ
| | Sample_contact_address | Winterthurerstr. 190
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8057
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM359nnn/GSM359573/suppl/GSM359573.CEL.gz
| | Sample_series_id | GSE14385
| | Sample_series_id | GSE14461
| | Sample_data_row_count | 54613
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
