|
| 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 |
When the HepG2 cells were 80% confluent, 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 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 24 and 48 hours of incubation with CsA or DMSO, 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 |
RNA was labeled using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Netherlands) according to the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
RNA was labeled using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Netherlands) according to the manufacturer’s protocol.
|
| Scan protocol |
Arrays were scanned using the Agilent Technologies Scanner. To quantify the signals, the images were processed to TXT files through the Feature Extraction Software v10.7.3.1 from Agilent Technologies.
|
| Description |
Ct_48h_IC20-24h_Ex.1
|
| Data processing |
The arrays were imported in R 2.15.2 (http://www.r-project.org) for quality control with an in-house developed pipeline and all but 1 microarrays were of high quality. The bad quality array and the array containing the paired sample were removed from further analyses. Further downstream analysis was performed by means of AgiMicroRna (Lopez-Romero, 2011) and the intensities were log2 transformed and quantile normalized.
|
| |
|
| 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 |
GPL17912 |
| Series (2) |
| GSE55880 |
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [miRNA] |
| GSE55883 |
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control |
|
