|
| Status |
Public on Oct 01, 2015 |
| Title |
MEF4F, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
MEF4F
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: B6
cell type: mouse embyronic fibroblasts (mEFs)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Minikit (Qiagen) according to manufacturer's recommendations.
|
| Label |
biotin
|
| Label protocol |
Illumina total PrepTM 96 RNA amplification kit.
|
| |
|
| Hybridization protocol |
According to Whole-Genome Gene Expression Direct Hybridization by Illumina.
|
| Scan protocol |
According to Whole-Genome Gene Expression Direct Hybridization by Illumina.
|
| Description |
Replicate 1
|
| 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 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 |
Dec 12, 2014 |
| Last update date |
Jan 15, 2022 |
| 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 |
GPL6887 |
| Series (1) |
| GSE64145 |
Breaking the first lineage barrier: Direct induction of trophoblast stem cells from murine fibroblasts |
|
