|
| Status |
Public on Dec 15, 2020 |
| Title |
HepG2 exposed to DMSO for 48 h, exposure 2, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
compound: DMSO
dose: 0.5percent
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 |
Trizol extraction was performed using the miRNAeasy kit from qiagen accoding 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 |
Gene expression data from HepG2 exposed to DMSO for 48 h, exposure 2, biological replicate 1
|
| Data processing |
Obtained data sets were re-annotated to the Brainarray custom CDF-file V22 ENSEMBL gene ID (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 R-scripts from ArrayAnalysis.org (Eijssen et al., 2013).
|
| |
|
| Submission date |
Dec 14, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Danyel Jennen |
| E-mail(s) |
danyel.jennen@maastrichtuniversity.nl
|
| Organization name |
Maastricht University
|
| Department |
Toxicogenomics
|
| Street address |
Universiteitssingel 40
|
| City |
Maastricht |
| ZIP/Postal code |
6229ER |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL29499 |
| Series (1) |
| GSE163130 |
Expression Profiles of HepG2 cells treated with 7 compounds |
|
