Search results for the GEO ID: GSE15633  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM391329 | GPL1261 |
|
CKO V3
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal conditional Keap1 knockout gene expression
|
| Sample_geo_accession | GSM391329
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391329/suppl/GSM391329.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391330 | GPL1261 |
|
CKO V4
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal conditional Keap1 knockout gene expression
|
| Sample_geo_accession | GSM391330
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391330/suppl/GSM391330.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391331 | GPL1261 |
|
CKO V5
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal conditional Keap1 knockout gene expression
|
| Sample_geo_accession | GSM391331
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391331/suppl/GSM391331.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391332 | GPL1261 |
|
CKO TP2
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
conditional Keap1 knockout mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391332
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391332/suppl/GSM391332.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391333 | GPL1261 |
|
CKO TP3
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
conditional Keap1 knockout mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391333
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391333/suppl/GSM391333.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391334 | GPL1261 |
|
CKO TP4
|
conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue
|
genotype: conditional keap1 knockout
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
conditional Keap1 knockout mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391334
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391334/suppl/GSM391334.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391335 | GPL1261 |
|
CKO Wild Type V1
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal genetic control wild-type gene expression
|
| Sample_geo_accession | GSM391335
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391335/suppl/GSM391335.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391336 | GPL1261 |
|
CKO Wild Type V2
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal genetic control wild-type gene expression
|
| Sample_geo_accession | GSM391336
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391336/suppl/GSM391336.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391337 | GPL1261 |
|
CKO Wild Type V3
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
Basal genetic control wild-type gene expression
|
| Sample_geo_accession | GSM391337
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391337/suppl/GSM391337.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391338 | GPL1261 |
|
CKO Wild Type TP2
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
genetic control wild-type mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391338
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391338/suppl/GSM391338.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391339 | GPL1261 |
|
CKO Wild Type TP3
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
genetic control wild-type mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391339
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391339/suppl/GSM391339.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
GSM391340 | GPL1261 |
|
CKO Wild Type TP4
|
genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue
|
genotype: genetic control for cko mice, alb-cre: Keap1(flox/+)
strain: c57bl/6j
gender: male
age: 9 weeks
tissue: Liver
|
genetic control wild-type mice treated with CDDO-Im gene expression
|
| Sample_geo_accession | GSM391340
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 10 2009
| | Sample_last_update_date | Apr 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later
| | Sample_growth_protocol_ch1 | no growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.
| | Sample_label_ch1 | ENZO BioArray HighYield RNA Transcript Labeling Kit
| | Sample_label_protocol_ch1 | cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
| | Sample_scan_protocol | Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
| | Sample_data_processing | The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed. The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas ,W,Kensler
| | Sample_contact_email | tkensler@jhsph.edu
| | Sample_contact_institute | Johns Hopkins School of Medicine
| | Sample_contact_address | 615 N Wolfe St SPH Rm E7541
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391340/suppl/GSM391340.CEL.gz
| | Sample_series_id | GSE15633
| | Sample_data_row_count | 45101
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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