Search results for the GEO ID: GSE17251  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM432139 | GPL570 |
|
Donor1_6h_Wy
|
Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 1
agent: Wy14643
time: 6h
gender: Male
age: 63 years old
|
no additional information
|
| Sample_geo_accession | GSM432139
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432139/suppl/GSM432139.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432140 | GPL570 |
|
Donor1_6h_DMSO
|
Primary hepatocytes isolated from Donor 1 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 1
agent: control
time: 6h
gender: Male
age: 63 years old
|
no additional information
|
| Sample_geo_accession | GSM432140
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432140/suppl/GSM432140.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432141 | GPL570 |
|
Donor1_24h_Wy
|
Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 1
agent: Wy14643
time: 24h
gender: Male
age: 63 years old
|
no additional information
|
| Sample_geo_accession | GSM432141
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432141/suppl/GSM432141.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432142 | GPL570 |
|
Donor1_24h_DMSO
|
Primary hepatocytes isolated from Donor 1 treated with DMSO for 24h
|
cell type: Primary hepatocytes
donor: 1
agent: control
time: 24h
gender: Male
age: 63 years old
|
no additional information
|
| Sample_geo_accession | GSM432142
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432142/suppl/GSM432142.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432143 | GPL570 |
|
Donor2_6h_Wy
|
Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 2
agent: Wy14643
time: 6h
gender: Male
age: 44 years old
|
no additional information
|
| Sample_geo_accession | GSM432143
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432143/suppl/GSM432143.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432144 | GPL570 |
|
Donor2_6h_DMSO
|
Primary hepatocytes isolated from Donor 2 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 2
agent: control
time: 6h
gender: Male
age: 44 years old
|
no additional information
|
| Sample_geo_accession | GSM432144
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432144/suppl/GSM432144.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432145 | GPL570 |
|
Donor2_24h_Wy
|
Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 2
agent: Wy14643
time: 24h
gender: Male
age: 44 years old
|
no additional information
|
| Sample_geo_accession | GSM432145
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432145/suppl/GSM432145.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432146 | GPL570 |
|
Donor2_24h_DMSO
|
Primary hepatocytes isolated from Donor 2 treated with DMSO for 24h
|
cell type: Primary hepatocytes
donor: 2
agent: control
time: 24h
gender: Male
age: 44 years old
|
no additional information
|
| Sample_geo_accession | GSM432146
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432146/suppl/GSM432146.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432147 | GPL570 |
|
Donor3_6h_Wy
|
Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 3
agent: Wy14643
time: 6h
gender: Female
age: 70 years old
|
no additional information
|
| Sample_geo_accession | GSM432147
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432147/suppl/GSM432147.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432148 | GPL570 |
|
Donor3_6h_DMSO
|
Primary hepatocytes isolated from Donor 3 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 3
agent: control
time: 6h
gender: Female
age: 70 years old
|
no additional information
|
| Sample_geo_accession | GSM432148
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432148/suppl/GSM432148.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432149 | GPL570 |
|
Donor3_24h_Wy
|
Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 3
agent: Wy14643
time: 24h
gender: Female
age: 70 years old
|
no additional information
|
| Sample_geo_accession | GSM432149
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432149/suppl/GSM432149.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432150 | GPL570 |
|
Donor3_24h_DMSO
|
Primary hepatocytes isolated from Donor 3 treated with DMSO for 24h
|
cell type: Primary hepatocytes
donor: 3
agent: control
time: 24h
gender: Female
age: 70 years old
|
no additional information
|
| Sample_geo_accession | GSM432150
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432150/suppl/GSM432150.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432151 | GPL570 |
|
Donor4_6h_Wy
|
Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 4
agent: Wy14643
time: 6h
gender: Female
age: 54 years old
|
no additional information
|
| Sample_geo_accession | GSM432151
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432151/suppl/GSM432151.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432152 | GPL570 |
|
Donor4_6h_DMSO
|
Primary hepatocytes isolated from Donor 4 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 4
agent: control
time: 6h
gender: Female
age: 54 years old
|
no additional information
|
| Sample_geo_accession | GSM432152
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432152/suppl/GSM432152.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432153 | GPL570 |
|
Donor4_24h_Wy
|
Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 4
agent: Wy14643
time: 24h
gender: Female
age: 54 years old
|
no additional information
|
| Sample_geo_accession | GSM432153
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432153/suppl/GSM432153.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432154 | GPL570 |
|
Donor4_24h_DMSO
|
Primary hepatocytes isolated from Donor 4 treated with DMSO for 24h
|
cell type: Primary hepatocytes
donor: 4
agent: control
time: 24h
gender: Female
age: 54 years old
|
no additional information
|
| Sample_geo_accession | GSM432154
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432154/suppl/GSM432154.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432155 | GPL570 |
|
Donor5_6h_Wy
|
Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 5
agent: Wy14643
time: 6h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432155
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432155/suppl/GSM432155.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432156 | GPL570 |
|
Donor5_6h_DMSO
|
Primary hepatocytes isolated from Donor 5 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 5
agent: control
time: 6h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432156
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432156/suppl/GSM432156.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432157 | GPL570 |
|
Donor5_24h_Wy
|
Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 5
agent: Wy14643
time: 24h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432157
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432157/suppl/GSM432157.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432158 | GPL570 |
|
Donor5_24h_DMSO
|
Primary hepatocytes isolated from Donor 5 treated with DMSO for 24h
|
cell type: Primary hepatocytes
donor: 5
agent: control
time: 24h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432158
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432158/suppl/GSM432158.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432159 | GPL570 |
|
Donor6_6h_Wy
|
Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 6h
|
cell type: Primary hepatocytes
donor: 6
agent: Wy14643
time: 6h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432159
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432159/suppl/GSM432159.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432160 | GPL570 |
|
Donor6_6h_DMSO
|
Primary hepatocytes isolated from Donor 6 treated with DMSO for 6h
|
cell type: Primary hepatocytes
donor: 6
agent: control
time: 6h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432160
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432160/suppl/GSM432160.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
| | |
|
GSM432161 | GPL570 |
|
Donor6_24h_Wy
|
Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 24h
|
cell type: Primary hepatocytes
donor: 6
agent: Wy14643
time: 24h
gender: Male
age: 73 years old
|
no additional information
|
| Sample_geo_accession | GSM432161
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432161/suppl/GSM432161.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
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GSM432162 | GPL570 |
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Donor6_24h_DMSO
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Primary hepatocytes isolated from Donor 6 treated with DMSO for 24h
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cell type: Primary hepatocytes
donor: 6
agent: control
time: 24h
gender: Male
age: 73 years old
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no additional information
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| Sample_geo_accession | GSM432162
| | Sample_status | Public on Sep 04 2009
| | Sample_submission_date | Jul 22 2009
| | Sample_last_update_date | Sep 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.
| | Sample_growth_protocol_ch1 | Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.
| | Sample_hyb_protocol | Hybridisation of 500ng 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 n 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 GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
| | 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/GSM432nnn/GSM432162/suppl/GSM432162.CEL.gz
| | Sample_series_id | GSE17251
| | Sample_series_id | GSE17254
| | Sample_data_row_count | 54675
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