|
| Status |
Public on Dec 08, 2010 |
| Title |
MEF, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast (MEF)
potency: unipotent
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion.
|
| Label |
biotin
|
| Label protocol |
500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol. Purified and labelled cRNA was hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare).
|
| Scan protocol |
Standard Illumina scanning protocol. Chips were scanned using the iScan reader (Illumina) and accompanying software.
|
| Description |
Biological replicate 1 of 2.
|
| Data processing |
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
|
| |
|
| Submission date |
Apr 26, 2010 |
| Last update date |
Jan 15, 2022 |
| Contact name |
Marcos J. Araúzo-Bravo |
| E-mail(s) |
mararabra@yahoo.co.uk
|
| Phone |
+34 943 00 6108
|
| Organization name |
Max Planck Institute for Molecular Biomedicine
|
| Department |
Cell and Developmental Biology
|
| Lab |
Computational Biology and Bionformatics
|
| Street address |
Rogentstrasse
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE21516 |
Direct Reprogramming of Fibroblasts into Epiblast Stem Cells |
|
