|
| Status |
Public on Jul 24, 2014 |
| Title |
Primary Mouse Hepatocytes exposed to 0.5 % v/v DMSO for 48h, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
primary mouse hepatocytes_0.5 % v/v DMSO for 48h
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl6
cell type: primary mouse hepatocytes
exposed to: 0.5 % v/v DMSO for 48h
|
| Treatment protocol |
After the recovery period (40-42 hours), the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO)
|
| Growth protocol |
Primary Mouse Hepatocytes were cultured in 6-well plates in a collagen-collagen sandwich and in the presence of serum-free culture medium supplemented with glucagon (7ng/mL), insulin (0.5 U/mL), 2% penicillin/streptomycin and hydrocortison (7.5 µg/mL). The cells were incubated at 37 C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated after 24 and 48 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 Affymetrix 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 Affymetrix GeneArray scanner.
|
| Description |
DMSO_48h_Exp1_34
|
| Data processing |
Obtained data sets were re-annotated to the MBNI Custom CDF-files v15.1 (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 Arrayanalysis.org web service.
The 'complete_data.txt' (of 17,370 data rows) contains ~60 of control probes, which are not included in the sample data table.
|
| |
|
| Submission date |
Mar 13, 2014 |
| Last update date |
Jul 24, 2014 |
| Contact name |
Wim Van den Hof |
| E-mail(s) |
vandenhof.wim@gmail.com
|
| 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 |
GPL15967 |
| Series (2) |
| GSE55881 |
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [RNA] |
| GSE55883 |
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control |
|
