Search results for the GEO ID: GSE9768  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM246400 | GPL570 |
|
CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 1
|
2 hours after 15 minute exposure to deoxycholic acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to deoxycholic acid, pH 4.5
|
| Sample_geo_accession | GSM246400
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246400/suppl/GSM246400.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246400/suppl/GSM246400.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246400/suppl/GSM246400.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246401 | GPL570 |
|
CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 1
|
6 hours after 15 minute exposure to deoxycholic acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 6 hours after exposure to deoxycholic acid, pH 4.5
|
| Sample_geo_accession | GSM246401
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246401/suppl/GSM246401.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246401/suppl/GSM246401.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246401/suppl/GSM246401.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246402 | GPL570 |
|
CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 2
|
2 hours after 15 minute exposure to deoxycholic acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to deoxycholic acid, pH 4.5
|
| Sample_geo_accession | GSM246402
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246402/suppl/GSM246402.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246402/suppl/GSM246402.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246402/suppl/GSM246402.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246403 | GPL570 |
|
CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 2
|
6 hours after 15 minute exposure to deoxycholic acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 6 hours after exposure to deoxycholic acid, pH 4.5
|
| Sample_geo_accession | GSM246403
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246403/suppl/GSM246403.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246403/suppl/GSM246403.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246403/suppl/GSM246403.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246404 | GPL570 |
|
CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 1
|
2 hours after 15 minute exposure to a mix of primary bile salts, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to a mix of primary bile salts, pH 4.5
|
| Sample_geo_accession | GSM246404
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246404/suppl/GSM246404.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246404/suppl/GSM246404.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246404/suppl/GSM246404.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246405 | GPL570 |
|
CP-A hTERT-primary bile mixture pH 4.5_6 hours_ rep 1
|
6 hours after 15 minute exposure to a mix of primary bile salts, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 6 hours after exposure to a mix of primary bile salts, pH 4.5
|
| Sample_geo_accession | GSM246405
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246405/suppl/GSM246405.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246405/suppl/GSM246405.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246405/suppl/GSM246405.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246406 | GPL570 |
|
CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 2
|
2 hours after 15 minute exposure to a mix of primary bile salts, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to a mix of primary bile salts, pH 4.5
|
| Sample_geo_accession | GSM246406
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246406/suppl/GSM246406.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246406/suppl/GSM246406.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246406/suppl/GSM246406.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246407 | GPL570 |
|
CP-A hTERT-acid pH 4.5_2 hours_ rep 1
|
2 hours after 15 minute exposure to acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to acid pH 4.5
|
| Sample_geo_accession | GSM246407
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246407/suppl/GSM246407.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246407/suppl/GSM246407.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246407/suppl/GSM246407.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246408 | GPL570 |
|
CP-A hTERT-acid pH 4.5_6 hours_ rep 1
|
6 hours after 15 minute exposure to acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 6 hours after exposure to acid pH 4.5
|
| Sample_geo_accession | GSM246408
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246408/suppl/GSM246408.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246408/suppl/GSM246408.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246408/suppl/GSM246408.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246409 | GPL570 |
|
CP-A hTERT control_rep 1
|
unexposed cells
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from unexposed cells
|
| Sample_geo_accession | GSM246409
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246409/suppl/GSM246409.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246409/suppl/GSM246409.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246409/suppl/GSM246409.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246410 | GPL570 |
|
CP-A hTERT-acid pH 4.5_2 hours_ rep 2
|
2 hours after 15 minute exposure to acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 2 hours after exposure to acid pH 4.5
|
| Sample_geo_accession | GSM246410
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246410/suppl/GSM246410.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246410/suppl/GSM246410.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246410/suppl/GSM246410.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246411 | GPL570 |
|
CP-A hTERT-acid pH 4.5_6 hours_ rep 2
|
6 hours after 15 minute exposure to acid, pH 4.5
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from 6 hours after exposure to acid pH 4.5
|
| Sample_geo_accession | GSM246411
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246411/suppl/GSM246411.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246411/suppl/GSM246411.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246411/suppl/GSM246411.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
| | |
|
GSM246412 | GPL570 |
|
CP-A hTERT control_rep 2
|
unexposed cells
|
CP-A hTERT Barrett's oesophagus cell line
Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations
|
Gene expression data from unexposed cells
|
| Sample_geo_accession | GSM246412
| | Sample_status | Public on Dec 05 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone. Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids. Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes. At the end of this time, cells were again washed twice with PBS and normal media replaced. For control flasks, media was also replaced. Cells were lysed for RNA extraction at 2 and 6 hours.
| | Sample_growth_protocol_ch1 | For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma). To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma). The volume was made up to 1L and was vacuum filtered into a sterile bottle. To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised. This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma). Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media. The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix 450 Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned using the Afftymetrix Scanner GCS3000
| | Sample_data_processing | The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Clare,,Donnellan
| | Sample_contact_email | clare.donnellan@usa.net
| | Sample_contact_phone | 0044 7973 472082
| | Sample_contact_department | Molecular Epidemiology
| | Sample_contact_institute | Leeds University
| | Sample_contact_address | LIGHT Laboratories
| | Sample_contact_city | Leeds University, Leeds
| | Sample_contact_state | West Yorkshire
| | Sample_contact_zip/postal_code | LS2 9JT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246412/suppl/GSM246412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246412/suppl/GSM246412.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246412/suppl/GSM246412.EXP.gz
| | Sample_series_id | GSE9768
| | Sample_data_row_count | 54675
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