|
| Status |
Public on Jan 27, 2015 |
| Title |
HepG2 exposed to DMSO for 48h, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatocellular carcinoma cell line
compound, dose: DMSO
time: 48h
|
| Treatment protocol |
When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO)
|
| 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 |
Total RNA was isolated after 12, 24, 48 and 72 hours of incubation with CsA or DMSO in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.
|
| 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
|
| Data processing |
Obtained data sets were re-annotated to the MBNI Custom CDF-files v14 (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the Arrayanalysis.org web service. The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls
|
| |
|
| Submission date |
Mar 29, 2013 |
| Last update date |
Jan 27, 2015 |
| Contact name |
Wim Van den Hof |
| E-mail(s) |
[email protected]
|
| Organization name |
Maastricht University
|
| Department |
Toxicogenomics
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| ZIP/Postal code |
P.O. Box 616, 6200 MD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16311 |
| Series (2) |
| GSE45635 |
Expression Profiles of HepG2 cells treated with Cyclosporin A and solvent control |
| GSE45802 |
Expression Profiles of mRNAs and microRNAs in HepG2 cells treated with Cyclosporin A and solvent control |
|
