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Sample GSM432155 Query DataSets for GSM432155
Status Public on Sep 04, 2009
Title Donor5_6h_Wy
Sample type RNA
 
Source name Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 6h
Organism Homo sapiens
Characteristics cell type: Primary hepatocytes
donor: 5
agent: Wy14643
time: 6h
gender: Male
age: 73 years old
Treatment protocol 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.
Growth protocol 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%.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.
Label biotin
Label protocol 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.
 
Hybridization 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).
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).
Description no additional information
Data processing Expression estimates were calculated using GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.
 
Submission date Jul 22, 2009
Last update date Sep 04, 2009
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL570
Series (2)
GSE17251 Comparative analysis of gene regulation by the transcription factor PPARα_human
GSE17254 Comparative analysis of gene regulation by the transcription factor PPARα between mouse and human

Data table header descriptions
ID_REF
VALUE GCRMA signal (log2)

Data table
ID_REF VALUE
1007_s_at 4.488337064
1053_at 5.750343546
117_at 3.373897968
121_at 6.529913382
1255_g_at 1.275478741
1294_at 3.037698646
1316_at 2.835242206
1320_at 3.001770275
1405_i_at 1.8219278
1431_at 6.56010792
1438_at 1.416133432
1487_at 6.946146858
1494_f_at 4.37737016
1552256_a_at 9.409192005
1552257_a_at 6.959669706
1552258_at 2.41142872
1552261_at 2.15683096
1552263_at 7.430368412
1552264_a_at 7.503424217
1552266_at 2.121963117

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM432155.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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