|
| Status |
Public on Dec 05, 2013 |
| Title |
PMH exposed to PBS for 48h, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
primary hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell line: PMH
treatment: PBS, 0.5%
time: 48h
|
| Treatment protocol |
After a recovery period of 40-42h, the Dulbecco's Modified Eagle's culture medium was replaced by culture medium containing cisplatin or a vehicle control (0.5% of PBS).
|
| Growth protocol |
Primary mouse hepatocytes were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates
|
| 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 Mouse Genome 430 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_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 16,395 probe sets represent 16,331 unique genes and 64 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 |
GPL15592 |
| Series (2) |
| GSE38123 |
Expression Profiles of PMH 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 |
|
