|
| Status |
Public on Jan 01, 2016 |
| Title |
iPS-I3-ep_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured cells
|
| Organism |
Sus scrofa |
| Characteristics |
reprogramming technique: Integrative
starting cell type: t(Y;14) fibroblasts
resulting cell type: I-iPS-like cells
culture conditions: piPS medium
cell line: I3
passage: early
|
| Growth protocol |
PEF were culture in F medium, all iPS-like cells were culture in piPS medium. Floating embryoïd bodies were cultured 10 days in in DIFF medium. For medium composition see the Material and Methods section of the associated publication.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell pellets of each sample was extracted in triplicate using the Nucleospin RNA kit (Macherey-Nagel). Quantity and quality of RNA was evaluated by NanoDrop dosage and Bioanalyser analysis (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Label, hybridation , scan and data extraction were performed by the GeT-Biopuces platform following manufacturer's intruction. Samples were then marked by Cyanine-3 fluorochrome and converted in cDNA before hybridization on the 60K customized chip from Agilent (Voillet et al., 2014).
|
| |
|
| Hybridization protocol |
Microarray hybridation oven according to manufacturer's instruction
|
| Scan protocol |
Image analysis using the Feature Extraction software (Agilent).
|
| Description |
Gene expression in I-iPS-like cells at early passages
I3ep_B
|
| Data processing |
Data were filtered to keep only spots of sufficient intensity and quality for at least 2 out of 3 technical replicates. Intensity values were log-transformed and normalized by the quantile normalization method. Differential analysis was then performed using the Limma package (Bioconductor). Threshold parameters were defined as follow: maximal adjusted p-value (Benjamini& Hochberg) of 0.01 and minimal log-fold change (lfc) of 2.
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
Jan 01, 2016 |
| Contact name |
Herve Acloque |
| E-mail(s) |
herve.acloque@toulouse.inra.fr
|
| Organization name |
INRA
|
| Department |
Animal Genetics
|
| Lab |
GenPhySE UMR1388
|
| Street address |
24 chemin de Borde Rouge
|
| City |
Castanet-Tolosan |
| ZIP/Postal code |
31326 |
| Country |
France |
| |
|
| Platform ID |
GPL20779 |
| Series (1) |
| GSE71792 |
Characterization of the gene expression profile of porcine iPS-like cells derived by two reprogramming techniques from translocated t(Y;14) fibroblasts |
|
