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Sample GSM935095 Query DataSets for GSM935095
Status Public on Dec 05, 2013
Title HepG2 exposed to PBS for 12h, biological rep 1
Sample type RNA
 
Source name hepatocellular carcinoma cell line
Organism Homo sapiens
Characteristics cell line: HepG2
treatment: PBS, 0.5%
time: 12h
Treatment protocol When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either 7µM of cisplatin or solvent ( 0.5% PBS)
Growth protocol HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.
Extracted molecule total RNA
Extraction protocol Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit
 
Hybridization protocol 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit
Scan protocol Arrays were scanned using genechip scanner 3000 7G
Description PBS_12h-Ex1
Data processing Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls
 
Submission date May 22, 2012
Last update date Dec 05, 2013
Contact name Linda Rieswijk
E-mail(s) linda.rieswijk@maastrichtuniversity.nl
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code 6229 ER
Country Netherlands
 
Platform ID GPL11084
Series (2)
GSE38122 Expression Profiles of HepG2 cells treated with 7µM of the genotoxic compound cisplatin
GSE38124 Characterization of cisplatin-induced transcriptomics responses in primary mouse hepatocytes, HepG2 cells and mouse embryonic stem cells shows a strong conservation of involved transcription factors

Data table header descriptions
ID_REF
VALUE Log2 of RMA intensity from MBNI custom annotation

Data table
ID_REF VALUE
1_at 8.140323394
2_at 13.68953389
9_at 8.434870019
10_at 6.350880603
12_at 12.36423949
13_at 6.755297034
14_at 10.00266942
15_at 5.240455211
16_at 10.15282359
18_at 10.76769909
19_at 10.36435397
20_at 6.616249156
21_at 5.967713269
22_at 9.340005187
23_at 10.55391836
24_at 5.115168114
25_at 9.2251052
26_at 3.704011986
27_at 7.168570623
28_at 4.676787273

Total number of rows: 17726

Table truncated, full table size 359 Kbytes.




Supplementary file Size Download File type/resource
GSM935095_LR10_HG-U133_Plus_2_.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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