|
| Status |
Public on Jun 04, 2012 |
| Title |
P19_non-RA-treated_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
non-treated P19.6 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19.6
cell type: embryonal carcinoma cells
background strain: C3H/HeHa
treatment: none
|
| Growth protocol |
P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos’ Modified Eagle’s Medium (DMEM) containing 10% fetal calf serum (GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen). Integrity and purity of the RNAs were controlled on an Agilent Bioanalyzer using the RNA 6000 Nano Assay (Agilent). Ten ug of selected samples exhibiting a RIN >9.8 were then subjected to cDNA synthesis using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and a mix of 50 pmol random hexamers and 50 pmol of Oligo-dT. cDNAs were then treated for 10 min at 37°C with 5 µg RNaseA (Invitrogen), purified through a phenol:chloroform:isoamyl alcohol extraction on Phase Lock light gels (Fisher Scientific) and then precipitated following a quality control on 250 ng cDNA on agarose/BET gels.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems (Services, Reykjavic) following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems (Services, Reykjavic) following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Standard NimbleGen protocols (scanned at NimbleGen services, Reykjavic). See www.nimblegen.com.
|
| Description |
This sample is of non-treated P19.6 cells. Second of three independent replicates used in this experiment, each constituted by a pool of three separate cultures.
P19.6 is an embryonal carcinoma mouse cell line produced by McBurney MW & Rogers BJ, Dev. Biol. 1982 (PMID 7056443).
|
| Data processing |
Raw data (.pair) were subjected to the RMA algorithm (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) with quantile settings (Bolstad et al. Bioinformatics 19(2):185) for background correction and normalization, as implemented within the ArrayStar software package (DNAstar, Inc.).
|
| |
|
| Submission date |
Feb 15, 2011 |
| Last update date |
Jun 04, 2012 |
| Contact name |
Aurelien Serandour |
| E-mail(s) |
aurelien.serandour@cruk.cam.ac.uk
|
| Phone |
00441223769723
|
| Organization name |
Université de Rennes 1
|
| Department |
UMR CNRS 6290
|
| Lab |
Equipe SP@RTE
|
| Street address |
Bâtiment 13, Campus de Beaulieu
|
| City |
Rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
| |
|
| Platform ID |
GPL13179 |
| Series (2) |
| GSE27334 |
Whole-genome gene expression level changes in P19.6 mouse embryonal carcinoma cells compared to P19.6 cells treated for 48 hours with all-trans retinoic acid |
| GSE27436 |
Dynamic hydroxymethylation of DNA marks differentiation-driven enhancers |
|
