Search results for the GEO ID: GSE40120  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM985983 | GPL339 |
|
wild-type_phenobarbitol_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: phenobarbitol
|
wild type mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985983
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985983/suppl/GSM985983_YZ04020401.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985984 | GPL339 |
|
wild-type_phenobarbitol_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: phenobarbitol
|
wild type mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985984
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985984/suppl/GSM985984_YZ04020402.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985985 | GPL339 |
|
CAR.KO_phenobarbitol_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: phenobarbitol
|
CAR knockout mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985985
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985985/suppl/GSM985985_YZ04020403.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985986 | GPL339 |
|
CAR.KO_phenobarbitol_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: phenobarbitol
|
CAR knockout mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985986
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985986/suppl/GSM985986_YZ04020404.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985987 | GPL339 |
|
CAR.AH_phenobarbitol_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: phenobarbitol
|
Human CAR transgenic mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985987
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985987/suppl/GSM985987_YZ04020405.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985988 | GPL339 |
|
CAR.AH_phenobarbitol_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: phenobarbitol
|
Human CAR transgenic mice treated with phenobarbitol
|
| Sample_geo_accession | GSM985988
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985988/suppl/GSM985988_YZ04020406.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985989 | GPL339 |
|
wild-type_CITCO_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
wild type mice treated with CITCO
|
| Sample_geo_accession | GSM985989
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985989/suppl/GSM985989_YZ04020407.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985990 | GPL339 |
|
wild-type_CITCO_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
wild type mice treated with CITCO
|
| Sample_geo_accession | GSM985990
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985990/suppl/GSM985990_YZ04020408.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985991 | GPL339 |
|
CAR.KO_CITCO_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
CAR knockout mice treated with CITCO
|
| Sample_geo_accession | GSM985991
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985991/suppl/GSM985991_YZ04020409.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985992 | GPL339 |
|
CAR.KO_CITCO_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
CAR knockout mice treated with CITCO
|
| Sample_geo_accession | GSM985992
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985992/suppl/GSM985992_YZ040204010.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985993 | GPL339 |
|
CAR.AH_CITCO_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
Human CAR transgenic mice treated with CITCO
|
| Sample_geo_accession | GSM985993
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985993/suppl/GSM985993_YZ040204011.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985994 | GPL339 |
|
CAR.AH_CITCO_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
|
Human CAR transgenic mice treated with CITCO
|
| Sample_geo_accession | GSM985994
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985994/suppl/GSM985994_YZ040204012.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985995 | GPL339 |
|
wild-type_corn oil_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: corn oil
|
wild type mice treated with corn oil
|
| Sample_geo_accession | GSM985995
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985995/suppl/GSM985995_YZ04021201.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985996 | GPL339 |
|
wild-type_corn oil_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: corn oil
|
wild type mice treated with corn oil
|
| Sample_geo_accession | GSM985996
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985996/suppl/GSM985996_YZ04021202.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985997 | GPL339 |
|
CAR.KO_corn oil_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: corn oil
|
CAR knockout mice treated with corn oil
|
| Sample_geo_accession | GSM985997
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985997/suppl/GSM985997_YZ04021203.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985998 | GPL339 |
|
CAR.KO_corn oil_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: corn oil
|
CAR knockout mice treated with corn oil
|
| Sample_geo_accession | GSM985998
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985998/suppl/GSM985998_YZ04021204.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM985999 | GPL339 |
|
CAR.AH_corn oil_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: corn oil
|
Human CAR transgenic mice treated with corn oil
|
| Sample_geo_accession | GSM985999
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM985nnn/GSM985999/suppl/GSM985999_YZ04021205.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986000 | GPL339 |
|
CAR.AH_corn oil_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: corn oil
|
Human CAR transgenic mice treated with corn oil
|
| Sample_geo_accession | GSM986000
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986000/suppl/GSM986000_YZ04021206.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986001 | GPL339 |
|
wild-type_TCPOBOP_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
wild type mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986001
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986001/suppl/GSM986001_YZ04021207.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986002 | GPL339 |
|
wild-type_TCPOBOP_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: wild-type
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
wild type mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986002
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986002/suppl/GSM986002_YZ04021208.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986003 | GPL339 |
|
CAR.KO_TCPOBOP_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
CAR knockout mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986003
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986003/suppl/GSM986003_YZ04021209.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986004 | GPL339 |
|
CAR.KO_TCPOBOP_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: mCAR knockout
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
CAR knockout mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986004
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986004/suppl/GSM986004_YZ040212010.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986005 | GPL339 |
|
CAR.AH_TCPOBOP_rep1
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
Human CAR transgenic mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986005
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986005/suppl/GSM986005_YZ040212011.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
| | |
|
GSM986006 | GPL339 |
|
CAR.AH_TCPOBOP_rep2
|
liver
|
strain: C57BL/6x129Sv
gender: female
genotype: hCAR transgenic in mCAR knockout background
ligand: TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene
|
Human CAR transgenic mice treated with TCPOBOP
|
| Sample_geo_accession | GSM986006
| | Sample_status | Public on Aug 15 2012
| | Sample_submission_date | Aug 14 2012
| | Sample_last_update_date | Aug 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection. The injections were given at 24 hour intervals at 10 am. Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3. 6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.
| | Sample_growth_protocol_ch1 | Mice were fed normal chow and housed with a 12 hour light/dark cycle. AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions. After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide. Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).
| | Sample_hyb_protocol | Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.
| | Sample_scan_protocol | Chips were scanned using an Affymetrix GeneChip Scanner 3000. Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)
| | Sample_data_processing | RMA normalization using R version 2.15.0 and affy version 1.34.0
| | Sample_platform_id | GPL339
| | Sample_contact_name | Scott,Andrew,Ochsner
| | Sample_contact_email | sochsner@bcm.edu
| | Sample_contact_phone | 713-798-6227
| | Sample_contact_laboratory | NURSA: Nuclear Receptor Signaling Atlas
| | Sample_contact_department | Molecular and Cellular Biology
| | Sample_contact_institute | Baylor College of Medicine
| | Sample_contact_address | One Baylor Plaza
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM986nnn/GSM986006/suppl/GSM986006_YZ040212012.CEL.gz
| | Sample_series_id | GSE40120
| | Sample_data_row_count | 22690
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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