|
| Status |
Public on Jul 29, 2009 |
| Title |
ESC rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic Stem Cells
potency: Pluripotent
|
| 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 |
400 ng of total DNA-free RNA was used as input for cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol. Quality-checked cRNA samples were hybridized as biological or technical duplicates for 18 h onto mouse-8 v2 expression BeadChips (Illumina), washed, and stained following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.
|
| Scan protocol |
Standard Illumina scanning protocol. Scanned following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.
|
| 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.
|
| |
|
| Submission date |
May 20, 2009 |
| 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) |
| GSE16178 |
Induction of Pluripotency in Adult Unipotent Germline Stem Cells |
|
