|
| Status |
Public on Jun 22, 2023 |
| Title |
0h rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
0h rep 1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cell
treatment: E1A induction
harvest time after induction: 0h
genetic background: mixed C57BL/6, C3H and CD1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
300 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: 14h)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Purified and labeled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina, USA) following the manufacturer’s instructions
|
| Scan protocol |
After the recommended washing,
the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.
|
| Description |
replicate 1
|
| Data processing |
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method
|
| |
|
| Submission date |
Jul 14, 2014 |
| Last update date |
Jun 22, 2023 |
| Contact name |
Marcos J. Araúzo-Bravo |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE59372 |
Defining the Sox2-independent reprogramming steps to pluripotency |
|
