Search results for the GEO ID: GSE20498  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM515085 | GPL341 |
|
Vehicle control, 2 hr, hepatocyte, biological replicate 1
|
Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
151_0mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515085
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515085/suppl/GSM515085.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515086 | GPL341 |
|
Vehicle control, 2 hr, hepatocyte, biological replicate 2
|
Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
152_0mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515086
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515086/suppl/GSM515086.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515087 | GPL341 |
|
Vehicle control, 2 hr, hepatocyte, biological replicate 3
|
Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
153_0mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515087
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515087/suppl/GSM515087.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515088 | GPL341 |
|
Vehicle control, 2 hr, hepatocyte, biological replicate 4
|
Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
154_0mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515088
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515088/suppl/GSM515088.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515089 | GPL341 |
|
Vehicle control, 2 hr, hepatocyte, biological replicate 5
|
Rat hepatocytes from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
155_0mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515089
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515089/suppl/GSM515089.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515090 | GPL341 |
|
50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 1
|
Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
176_50mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515090
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515090/suppl/GSM515090.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515091 | GPL341 |
|
50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 2
|
Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
177_50mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515091
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515091/suppl/GSM515091.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515092 | GPL341 |
|
50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 3
|
Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
178_50mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515092
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515092/suppl/GSM515092.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515093 | GPL341 |
|
50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 4
|
Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
179_50mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515093
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515093/suppl/GSM515093.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515094 | GPL341 |
|
50 mg/kg ANIT, 2 hr, hepatocyte, biological replicate 5
|
Rat hepatocytes from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
180_50mg_2hr_hepatocyte.CEL
|
| Sample_geo_accession | GSM515094
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515094/suppl/GSM515094.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515095 | GPL341 |
|
Vehicle control, 2 hr, bile duct, biological replicate 1
|
Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
51_0mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515095
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515095/suppl/GSM515095.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515096 | GPL341 |
|
Vehicle control, 2 hr, bile duct, biological replicate 2
|
Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
52_0mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515096
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515096/suppl/GSM515096.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515097 | GPL341 |
|
Vehicle control, 2 hr, bile duct, biological replicate 3
|
Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
53_0mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515097
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515097/suppl/GSM515097.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515098 | GPL341 |
|
Vehicle control, 2 hr, bile duct, biological replicate 4
|
Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
54_0mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515098
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515098/suppl/GSM515098.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515099 | GPL341 |
|
Vehicle control, 2 hr, bile duct, biological replicate 5
|
Rat bile ducts from animal 2 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
55_0mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515099
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515099/suppl/GSM515099.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515100 | GPL341 |
|
50 mg/kg ANIT, 2 hr, bile duct, biological replicate 1
|
Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
76_50mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515100
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515100/suppl/GSM515100.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515101 | GPL341 |
|
50 mg/kg ANIT, 2 hr, bile duct, biological replicate 2
|
Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
77_50mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515101
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515101/suppl/GSM515101.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515102 | GPL341 |
|
50 mg/kg ANIT, 2 hr, bile duct, biological replicate 3
|
Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
78_50mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515102
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515102/suppl/GSM515102.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515103 | GPL341 |
|
50 mg/kg ANIT, 2 hr, bile duct, biological replicate 4
|
Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
79_50mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515103
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515103/suppl/GSM515103.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515104 | GPL341 |
|
50 mg/kg ANIT, 2 hr, bile duct, biological replicate 5
|
Rat bile ducts from animal 2 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
80_50mg_2hr_bileduct.CEL
|
| Sample_geo_accession | GSM515104
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515104/suppl/GSM515104.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515105 | GPL341 |
|
Vehicle control, 6 hr, hepatocyte, biological replicate 1
|
Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
157_0mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515105
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515105/suppl/GSM515105.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515106 | GPL341 |
|
Vehicle control, 6 hr, hepatocyte, biological replicate 2
|
Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
156_0mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515106
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515106/suppl/GSM515106.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515107 | GPL341 |
|
Vehicle control, 6 hr, hepatocyte, biological replicate 3
|
Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
158_0mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515107
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515107/suppl/GSM515107.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515108 | GPL341 |
|
Vehicle control, 6 hr, hepatocyte, biological replicate 4
|
Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
159_0mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515108
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515108/suppl/GSM515108.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515109 | GPL341 |
|
Vehicle control, 6 hr, hepatocyte, biological replicate 5
|
Rat hepatocytes from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
160_0mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515109
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515109/suppl/GSM515109.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515110 | GPL341 |
|
50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 1
|
Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
181_50mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515110
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515110/suppl/GSM515110.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515111 | GPL341 |
|
50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 2
|
Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
182_50mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515111
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515111/suppl/GSM515111.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515112 | GPL341 |
|
50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 3
|
Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
183_50mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515112
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515112/suppl/GSM515112.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515113 | GPL341 |
|
50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 4
|
Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
184_50mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515113
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515113/suppl/GSM515113.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515114 | GPL341 |
|
50 mg/kg ANIT, 6 hr, hepatocyte, biological replicate 5
|
Rat hepatocytes from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: liver
cell type: hepatocyes
isolation method: Laser Capture Microdissection
|
Gene expression data
185_50mg_6hr_Hep.CEL
|
| Sample_geo_accession | GSM515114
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515114/suppl/GSM515114.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515115 | GPL341 |
|
Vehicle control, 6 hr, bile duct, biological replicate 1
|
Rat bile ducts from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
56_0mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515115
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515115/suppl/GSM515115.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515116 | GPL341 |
|
Vehicle control, 6 hr, bile duct, biological replicate 2
|
Rat bile ducts from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
57_0mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515116
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515116/suppl/GSM515116.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515117 | GPL341 |
|
Vehicle control, 6 hr, bile duct, biological replicate 3
|
Rat bile ducts from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
58_0mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515117
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515117/suppl/GSM515117.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515118 | GPL341 |
|
Vehicle control, 6 hr, bile duct, biological replicate 4
|
Rat bile ducts from animal 6 hr after dosing with the vehicle, 10 ml/kg corn oil
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
59_0mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515118
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515118/suppl/GSM515118.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515119 | GPL341 |
|
50 mg/kg ANIT, 6 hr, bile duct, biological replicate 1
|
Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
81_50mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515119
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515119/suppl/GSM515119.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515120 | GPL341 |
|
50 mg/kg ANIT, 6 hr, bile duct, biological replicate 2
|
Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
82_50mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515120
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515120/suppl/GSM515120.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515121 | GPL341 |
|
50 mg/kg ANIT, 6 hr, bile duct, biological replicate 3
|
Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
83_50mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515121
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515121/suppl/GSM515121.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515122 | GPL341 |
|
50 mg/kg ANIT, 6 hr, bile duct, biological replicate 4
|
Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
84_50mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515122
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515122/suppl/GSM515122.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
GSM515123 | GPL341 |
|
50 mg/kg ANIT, 6 hr, bile duct, biological replicate 5
|
Rat bile ducts from animal 6 hr after dosing with ANIT in the vehicle
|
strain: Sprague Dawley
age: 8 weeks old
tissue: bile duct
isolation method: Laser Capture Microdissection
|
Gene expression data
85_50mg_6hr_Bileduct.CEL
|
| Sample_geo_accession | GSM515123
| | Sample_status | Public on Feb 24 2010
| | Sample_submission_date | Feb 23 2010
| | Sample_last_update_date | Feb 23 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, rats were treated with ANIT prepared in corn oil at 50 mg/kg or corn oil alone.
| | Sample_growth_protocol_ch1 | Described in detail in Cullen et.al., Toxicologic Pathology 2010. Briefly, 8 week old Sprague Dawley rats were used. Groups of 5 treated and 5 control rats were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA isolation was performed using the Picopure RNA Isolation kit according to protocol from Molecular Devices Corp.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified and labeled using the NuGen Ovation RNA Amplification System V2 and FL-Ovation cDNA Biotin Module V2 kits from NuGen Technologies
| | Sample_hyb_protocol | Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat RAE230A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
| | Sample_data_processing | First, a log2-transformed signal matrix with RMA and additional QC is generated using ArrayStudio 3.5. Differentially expressed probesets were identified using the integrated pipeline in Resolver RatioBuild which combines signal quantification and detection of differential expression in Rosetta Resolver Version 5.1 (Rosetta Biosoftware, Seattle , WA). Rosetta Resolver incorporates an error model that captures the variance-intensity for Affymetrix GeneChips which conservatively estimates intensity error and then utilizes this value to stabilize the variance estimation. (Weng et al., 2006) The performance of Resolver's error model for signal quantification and detection of differentially expressed genes was among the best of signal quantification and statistical methods evaluated by Vardhanabhuti et al. (Vardhanabhuti et al., 2006) In our study each treatment group was compared with the concurrent control group, with the output containing fold-changes relative to control and p-values for all probesets interrogated. These final processed ratio data are presented in supplementary files on the Series record.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Neal,F,Cariello
| | Sample_contact_email | Neal.F.Cariello@gsk.com
| | Sample_contact_phone | 919 483 6782
| | Sample_contact_laboratory | Investigative Toxicology and Pathology
| | Sample_contact_department | Safety Assessment
| | Sample_contact_institute | GlaxoSmithKline
| | Sample_contact_address | 5 Moore Drive, Bldg 9, Rom 2011
| | Sample_contact_city | Research Triangle Park
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM515nnn/GSM515123/suppl/GSM515123.CEL.gz
| | Sample_series_id | GSE20498
| | Sample_data_row_count | 15923
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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