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Sample GSM935103 Query DataSets for GSM935103
Status Public on Dec 05, 2013
Title HepG2 exposed to PBS for 48h, biological rep 3
Sample type RNA
 
Source name hepatocellular carcinoma cell line
Organism Homo sapiens
Characteristics cell line: HepG2
treatment: PBS, 0.5%
time: 48h
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_48h-Ex3
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 8.304065514
2_at 13.65217912
9_at 8.0688077
10_at 5.910745831
12_at 13.66166782
13_at 6.5181409
14_at 10.15377542
15_at 5.36105945
16_at 10.48912612
18_at 10.89225123
19_at 10.24683814
20_at 6.461709831
21_at 5.651378141
22_at 9.555000888
23_at 10.53276778
24_at 5.269667028
25_at 9.204711563
26_at 3.560079648
27_at 7.295052993
28_at 4.790992545

Total number of rows: 17726

Table truncated, full table size 359 Kbytes.




Supplementary file Size Download File type/resource
GSM935103_LR25_HG-U133_Plus_2_.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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