Search results for the GEO ID: GSE17925  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM447829 | GPL1261 |
|
hAHR-mouse hepatocytes DMSO treated biological rep 1
|
Control treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from DMSO treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447829
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447829/suppl/GSM447829.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447829/suppl/GSM447829.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447830 | GPL1261 |
|
hAHR-mouse hepatocytes DMSO treated biological rep 2
|
Control treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from DMSO treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447830
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447830/suppl/GSM447830.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447830/suppl/GSM447830.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447831 | GPL1261 |
|
hAHR-mouse hepatocytes DMSO treated biological rep 3
|
Control treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from DMSO treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447831
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447831/suppl/GSM447831.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447831/suppl/GSM447831.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447832 | GPL1261 |
|
hAHR-mouse hepatocytes 10nM TCDD treated biological replicate 1
|
TCDD treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447832
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447832/suppl/GSM447832.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447832/suppl/GSM447832.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447833 | GPL1261 |
|
hAHR-mouse hepatocytes 10nM TCDD treated biological replicate 2
|
TCDD treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447833
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447833/suppl/GSM447833.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447833/suppl/GSM447833.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447834 | GPL1261 |
|
hAHR-mouse hepatocytes 10nM TCDD treated biological replicate 3
|
TCDD treated hAHR-mouse hepatocytes
|
strain: B6.Cg-Ahrtm3.1Bra Tg (Alb-cre, Ttr-AHR)1Ghp
genome/variation: Human AHR
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated human AHR expressing mouse hepatocytes
|
| Sample_geo_accession | GSM447834
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447834/suppl/GSM447834.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447834/suppl/GSM447834.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447835 | GPL1261 |
|
C57BL6/J-mouse hepatocytes DMSO treated biological rep1
|
Control treated C57BL6/J hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM DMSO treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447835
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447835/suppl/GSM447835.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447835/suppl/GSM447835.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447836 | GPL1261 |
|
C57BL6/J-mouse hepatocytes DMSO treated biological rep2
|
Control treated C57BL6/J hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM DMSO treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447836
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447836/suppl/GSM447836.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447836/suppl/GSM447836.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447837 | GPL1261 |
|
C57BL6/J-mouse hepatocytes DMSO treated biological rep3
|
Control treated C57BL6/J hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM DMSO treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447837
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447837/suppl/GSM447837.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447837/suppl/GSM447837.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447838 | GPL1261 |
|
C57BL6/J-mouse hepatocytes 10nM TCDD treated biological rep1
|
TCDD treated C57BL6/J mouse hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447838
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447838/suppl/GSM447838.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447838/suppl/GSM447838.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447839 | GPL1261 |
|
C57BL6/J-mouse hepatocytes 10nM TCDD treated biological rep2
|
TCDD treated C57BL6/J mouse hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447839
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447839/suppl/GSM447839.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447839/suppl/GSM447839.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
GSM447840 | GPL1261 |
|
C57BL6/J-mouse hepatocytes 10nM TCDD treated biological rep3
|
TCDD treated C57BL6/J mouse hepatocytes
|
strain: C57BL6/J
genome/variation: wild type
tissue type: liver
cell type: hepatocytes
|
Gene expression data from 10nM TCDD treated C57BL6/J mouse hepatocytes
|
| Sample_geo_accession | GSM447840
| | Sample_status | Public on Sep 03 2009
| | Sample_submission_date | Sep 01 2009
| | Sample_last_update_date | Sep 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Hepatocytes were treated with 10nM TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) or DMSO vehicle control for 6h.
| | Sample_growth_protocol_ch1 | Primary hepatocytes were grown for 48h in long-term hepatocyte culture media [Hepatozyme-SFM (Invitrogen), 2.5% dimethyl sulfoxide, 10 nM dexamethasone, 100 IU/ml penicillin, and 100 µg/ml streptomycin] in a 37°C incubator at 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions with additional purification using RNeasy mini columns (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10ug of cRNA were hybridized for 16h at 45C on GeneChip Mouse Genome 430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | GeneChip® Operating Software was used to preprocess CAB/CEL files generated (Affymetrix Expression Console Software 1.1). Arrays were normalized using the Probe Logarithmic intensity Error Approximation MM algorithm (PLIER-MM) with default settings.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gary,H,Perdew
| | Sample_contact_institute | The Pennsylvania State University
| | Sample_contact_address | 309A Life Sciences Building
| | Sample_contact_city | Univeristy Park
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 16802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447840/suppl/GSM447840.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM447nnn/GSM447840/suppl/GSM447840.CHP.gz
| | Sample_series_id | GSE17925
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
