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Search results for the GEO ID: GSE25547

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GSM627985

GPL570

HepG2 cells_control_rep1

HepG2 cells treated with vehicle (DMSO)

cell line: HepG2 cell type: hepatoma treatment: DMSO vehicle

A125_01_ctr

Sample_geo_accession	GSM627985
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627985/suppl/GSM627985.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627986

GPL570

HepG2 cells_control_rep2

HepG2 cells treated with vehicle (DMSO)

cell line: HepG2 cell type: hepatoma treatment: DMSO vehicle

A125_02A_ctr

Sample_geo_accession	GSM627986
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627986/suppl/GSM627986.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627987

GPL570

HepG2 cells_control_rep3

HepG2 cells treated with vehicle (DMSO)

cell line: HepG2 cell type: hepatoma treatment: DMSO vehicle

A125_03_ctr

Sample_geo_accession	GSM627987
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627987/suppl/GSM627987.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627988

GPL570

HepG2 cells_GW7647_6h_rep1

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 6h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 6 hr

A125_04_GW6

Sample_geo_accession	GSM627988
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627988/suppl/GSM627988.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627989

GPL570

HepG2 cells_GW7647_6h_rep2

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 6h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 6 hr

A125_05_GW6

Sample_geo_accession	GSM627989
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627989/suppl/GSM627989.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627990

GPL570

HepG2 cells_GW7647_6h_rep3

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 6h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 6 hr

A125_06_GW6

Sample_geo_accession	GSM627990
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627990/suppl/GSM627990.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627991

GPL570

HepG2 cells_GW7647_24h_rep1

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 24h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 24 hr

A125_07_GW24

Sample_geo_accession	GSM627991
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627991/suppl/GSM627991.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627992

GPL570

HepG2 cells_GW7647_24h_rep2

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 24h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 24 hr

A125_08_GW24

Sample_geo_accession	GSM627992
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627992/suppl/GSM627992.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

GSM627993

GPL570

HepG2 cells_GW7647_24h_rep3

HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 24h

cell line: HepG2 cell type: hepatoma treatment: PPARα agonist GW7647 treatment duration: 24 hr

A125_09_GW24

Sample_geo_accession	GSM627993
Sample_status	Public on Nov 23 2010
Sample_submission_date	Nov 22 2010
Sample_last_update_date	Nov 22 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.
Sample_growth_protocol_ch1	HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using RMA in Bioconductor.
Sample_platform_id	GPL570
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM627nnn/GSM627993/suppl/GSM627993.CEL.gz
Sample_series_id	GSE25547
Sample_data_row_count	54675

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