|
| Status |
Public on Jan 13, 2015 |
| Title |
Fu_2mM(2)_48h |
| Sample type |
RNA |
| |
|
| Source name |
hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatocellular carcinoma
tissue: liver
compound and dose: 2mM Furan_48h_Biological replicate 2
time (h): 48
|
| Treatment protocol |
When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing, or fresh medium containing a genotoxic of non-genotoxic carcinogen
|
| 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 was used. The GeneTitan arrays were hybridized, washed and stained using the GeneTitan hybridization, wash and stain kit for 3’ IVT Arrays and GeneTitan Operating Software and scanned by means of an Affymetrix GeneTitan scanner
|
| Scan protocol |
Arrays were scanned with the GeneTitan scanner
|
| Description |
Effect of Furan on mRNA levels in HepG2 cells
I_48h_FU_2
|
| 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).
|
| |
|
| Submission date |
Jun 04, 2014 |
| Last update date |
Jan 13, 2015 |
| Contact name |
Lize Deferme |
| E-mail(s) |
l.deferme@maastrichtuniversity.nl
|
| Organization name |
Maastricht University
|
| Department |
TGX
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6200MD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18756 |
| Series (1) |
| GSE58235 |
Expression Profiles of HepG2 cells treated with following compounds: Azathriopine, Furan, Tetradecanoyl phorbol acetate, Tetrachloroethylene, Diazinon and Dmannitol |
|
| Relations |
| Reanalysis of |
GSM715352 |
