Result

Search results for the GEO ID: GSE15433

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM387050

GPL1261

NIH-CAR AdHA-PPARg2 replicate1

NIH-CAR cells transduced with adenovirus expressing full length PPARg2 treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387050
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387050/suppl/GSM387050.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387051

GPL1261

NIH-CAR AdHA-PPARg2 replicate2

NIH-CAR cells transduced with adenovirus expressing full length PPARg2 treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387051
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387051/suppl/GSM387051.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387052

GPL1261

NIH-CAR AdHA-PPARg2 replicate3

NIH-CAR cells transduced with adenovirus expressing full length PPARg2 treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387052
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387052/suppl/GSM387052.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387053

GPL1261

NIH-CAR AdEmpty replicate1

NIH-CAR cells transduced with adenovirus containing empty vector followed by addition of vehicle (DMSO)

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387053
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387053/suppl/GSM387053.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387054

GPL1261

NIH-CAR AdEmpty replicate2

NIH-CAR cells transduced with adenovirus containing empty vector followed by addition of vehicle (DMSO)

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387054
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387054/suppl/GSM387054.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387055

GPL1261

NIH-CAR AdEmpty replicate3

NIH-CAR cells transduced with adenovirus containing empty vector followed by addition of vehicle (DMSO)

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387055
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387055/suppl/GSM387055.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387056

GPL1261

NIH-CAR AdHA-PPARgCDE replicate1

NIH-CAR cells transduced with adenovirus expressing truncated PPARgamma2 lacking the A/B-domain treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387056
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387056/suppl/GSM387056.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387057

GPL1261

NIH-CAR AdHA-PPARgCDE replicate2

NIH-CAR cells transduced with adenovirus expressing truncated PPARgamma2 lacking the A/B-domain treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387057
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387057/suppl/GSM387057.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

GSM387058

GPL1261

NIH-CAR AdHA-PPARgCDE replicate3

NIH-CAR cells transduced with adenovirus expressing truncated PPARgamma2 lacking the A/B-domain treated with rosiglitazone

age: passage 12 cell line: NIH 3T3

n/a

Sample_geo_accession	GSM387058
Sample_status	Public on Mar 27 2009
Sample_submission_date	Mar 27 2009
Sample_last_update_date	Mar 30 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Adenovirus was suspended in medium and added to NIH-CAR cells at 80% confluency. After 2 h of transduction, the virus-containing medium was removed and new medium containing either only the vehicle dimethyl sulfoxide (DMSO) or 1 μM of the PPARg-specific agonist rosiglitazone/BRL49653.
Sample_growth_protocol_ch1	NIH-CAR cells were cultured in DMEM (Gibco) supplemented with 10% calf serum (Fischer Scientific PAA)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The adenovirally transduced NIH-CAR cells were harvested in 500 μl TRIzol. Total RNA was extracted by addition of chloroform and precipitated with isopropanol and centrifugation. The pellet was washed with 75 % ethanol and redissolved in diethyl pyrocarbonate (DEPC) treated water. The RNA samples were purified further on RNAeasy columns (Qiagen) and the integrity and purity of the RNA was verified with an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Two micrograms of total RNA was used to synthesize double-stranded cDNA with the one-cycle cDNA synthesis Kit (Affymetix Inc.) using an oligo(dT) primer containing a T7 RNA polymerase promoter (Affymetrix Inc.). The cDNA was purified using the GeneChip clean-up module (Affymetrix Inc.) and used as the template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (IVT labeling Kit; Affymetrix Inc.).
Sample_hyb_protocol	After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), 15 μg of labeled cRNA was hybridized for 16 h to the Mouse 430 2.0 array (Affymetrix Inc.)
Sample_scan_protocol	Hybridized arrays were scanned using the Affymetrix GeneChip® Scanner 3000
Sample_data_processing	The raw intensity data was normalized using the RMA algorithm implemented with the Bioconductor affy package using R version 2.5.0.
Sample_platform_id	GPL1261
Sample_contact_name	Susanne,,Mandrup
Sample_contact_email	s.mandrup@bmb.sdu.dk
Sample_contact_phone	+45 6550 2340
Sample_contact_department	Biochemistry and Molecular Biology
Sample_contact_institute	University of Southern Denmark
Sample_contact_address	Campusvej 55
Sample_contact_city	Odense M
Sample_contact_zip/postal_code	5230
Sample_contact_country	Denmark
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM387nnn/GSM387058/suppl/GSM387058.CEL.gz
Sample_series_id	GSE15433
Sample_data_row_count	45101

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