Search results for the GEO ID: GSE14554  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM364089 | GPL85 |
|
Rat1_Control_0
|
Rat Pool 1, vehicle control
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: Vehicle Control (0.5% DMSO)
Dose: NA
|
Rat Pool 1, vehicle control
|
| Sample_geo_accession | GSM364089
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364089/suppl/GSM364089.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364090 | GPL85 |
|
Rat2_Control_0
|
Rat Pool 2, vehicle control
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: Vehicle Control (0.5% DMSO)
Dose: NA
|
Rat Pool 2, vehicle control
|
| Sample_geo_accession | GSM364090
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364090/suppl/GSM364090.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364091 | GPL85 |
|
Rat1_TCDD_14
|
Rat Pool 1, -14logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -14logM
|
Rat Pool 1, -14logM TCDD
|
| Sample_geo_accession | GSM364091
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364091/suppl/GSM364091.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364092 | GPL85 |
|
Rat2_TCDD_14
|
Rat Pool 2, -14logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -14logM
|
Rat Pool 2, -14logM TCDD
|
| Sample_geo_accession | GSM364092
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364092/suppl/GSM364092.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364093 | GPL85 |
|
Rat1_TCDD_12
|
Rat Pool 1, -12logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -12logM
|
Rat Pool 1, -12logM TCDD
|
| Sample_geo_accession | GSM364093
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364093/suppl/GSM364093.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364094 | GPL85 |
|
Rat2_TCDD_12
|
Rat Pool 2, -12logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -12logM
|
Rat Pool 2, -12logM TCDD
|
| Sample_geo_accession | GSM364094
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364094/suppl/GSM364094.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364095 | GPL85 |
|
Rat1_TCDD_10
|
Rat Pool 1, -10logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -10logM
|
Rat Pool 1, -10logM TCDD
|
| Sample_geo_accession | GSM364095
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364095/suppl/GSM364095.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364096 | GPL85 |
|
Rat2_TCDD_11
|
Rat Pool 2, -11logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -11logM
|
Rat Pool 2, -11logM TCDD
|
| Sample_geo_accession | GSM364096
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364096/suppl/GSM364096.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364097 | GPL85 |
|
Rat1_TCDD_8
|
Rat Pool 1, -8logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -8logM
|
Rat Pool 1, -8logM TCDD
|
| Sample_geo_accession | GSM364097
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364097/suppl/GSM364097.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364098 | GPL85 |
|
Rat2_TCDD_10
|
Rat Pool 2, -10logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -10logM
|
Rat Pool 2, -10logM TCDD
|
| Sample_geo_accession | GSM364098
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364098/suppl/GSM364098.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364099 | GPL85 |
|
Rat1_TCDD_6.5
|
Rat Pool 1, -6.5logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -6.5logM
|
Rat Pool 1, -6.5logM TCDD
|
| Sample_geo_accession | GSM364099
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364099/suppl/GSM364099.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364100 | GPL85 |
|
Rat2_TCDD_9
|
Rat Pool 2, -9logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -9logM
|
Rat Pool 2, -9logM TCDD
|
| Sample_geo_accession | GSM364100
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364100/suppl/GSM364100.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364101 | GPL85 |
|
Rat1_PCB126_12
|
Rat Pool 1, -12logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -12logM
|
Rat Pool 1, -12logM PCB 126
|
| Sample_geo_accession | GSM364101
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364101/suppl/GSM364101.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364102 | GPL85 |
|
Rat2_TCDD_8
|
Rat Pool 2, -8logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -8logM
|
Rat Pool 2, -8logM TCDD
|
| Sample_geo_accession | GSM364102
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364102/suppl/GSM364102.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364103 | GPL85 |
|
Rat1_PCB126_10
|
Rat Pool 1, -10logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -10logM
|
Rat Pool 1, -10logM PCB 126
|
| Sample_geo_accession | GSM364103
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364103/suppl/GSM364103.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364104 | GPL85 |
|
Rat2_TCDD_6.5
|
Rat Pool 2, -6.5logM TCDD
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: TCDD
Dose: -6.5logM
|
Rat Pool 2, -6.5logM TCDD
|
| Sample_geo_accession | GSM364104
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364104/suppl/GSM364104.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364105 | GPL85 |
|
Rat1_PCB126_8
|
Rat Pool 1, -8logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -8logM
|
Rat Pool 1, -8logM PCB 126
|
| Sample_geo_accession | GSM364105
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364105/suppl/GSM364105.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364106 | GPL85 |
|
Rat2_PCB126_12
|
Rat Pool 2, -12logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -12logM
|
Rat Pool 2, -12logM PCB 126
|
| Sample_geo_accession | GSM364106
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364106/suppl/GSM364106.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364107 | GPL85 |
|
Rat1_PCB126_6
|
Rat Pool 1, -6logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -6logM
|
Rat Pool 1, -6logM PCB 126
|
| Sample_geo_accession | GSM364107
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364107/suppl/GSM364107.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364108 | GPL85 |
|
Rat2_PCB126_11
|
Rat Pool 2, -11logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -11logM
|
Rat Pool 2, -11logM PCB 126
|
| Sample_geo_accession | GSM364108
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364108/suppl/GSM364108.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364109 | GPL85 |
|
Rat1_PCB126_5
|
Rat Pool 1, -5logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -5logM
|
Rat Pool 1, -5logM PCB 126
|
| Sample_geo_accession | GSM364109
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364109/suppl/GSM364109.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364110 | GPL85 |
|
Rat2_PCB126_10
|
Rat Pool 2, -10logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -10logM
|
Rat Pool 2, -10logM PCB 126
|
| Sample_geo_accession | GSM364110
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364110/suppl/GSM364110.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364111 | GPL85 |
|
Rat2_PCB126_9
|
Rat Pool 2, -9logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -9logM
|
Rat Pool 2, -9logM PCB 126
|
| Sample_geo_accession | GSM364111
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364111/suppl/GSM364111.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364112 | GPL85 |
|
Rat2_PCB126_8
|
Rat Pool 2, -8logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -8logM
|
Rat Pool 2, -8logM PCB 126
|
| Sample_geo_accession | GSM364112
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364112/suppl/GSM364112.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364113 | GPL85 |
|
Rat2_PCB126_6
|
Rat Pool 2, -6logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -6logM
|
Rat Pool 2, -6logM PCB 126
|
| Sample_geo_accession | GSM364113
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364113/suppl/GSM364113.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
GSM364114 | GPL85 |
|
Rat2_PCB126_5
|
Rat Pool 2, -5logM PCB 126
|
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: PCB 126
Dose: -5logM
|
Rat Pool 2, -5logM PCB 126
|
| Sample_geo_accession | GSM364114
| | Sample_status | Public on Aug 19 2009
| | Sample_submission_date | Jan 23 2009
| | Sample_last_update_date | Aug 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_growth_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | GeneChips were hybridized according to the standard Affymetrix protocol
| | Sample_scan_protocol | GeneChips were scanned according to the standard Affymetrix protocol
| | Sample_data_processing | All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Erik,A,Carlson
| | Sample_contact_email | carlson@ge.com
| | Sample_contact_institute | General Electric
| | Sample_contact_address | 1 Research Circle
| | Sample_contact_city | Niskayuna
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 12309
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM364nnn/GSM364114/suppl/GSM364114.CEL.gz
| | Sample_series_id | GSE14554
| | Sample_series_id | GSE14555
| | Sample_data_row_count | 8799
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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