|
| Status |
Public on Oct 24, 2011 |
| Title |
hNanog iPS 3 |
| Sample type |
RNA |
| |
|
| Source name |
human Nanog iPS 3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: nanog iPS cells
strain: E14Tg2A (129)
|
| Growth protocol |
iPS and ES cells were cultured in N2B27 medium (Stem Cell Sciences, SCS-SF-NB-02) supplemented with LIF and 2i inhibitors (Ying et al., 2008), CHIR99021 (3μM) and PD0325901 (1μM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Amplification and labeling of RNA were performed according to the TotalPrep-96 RNA Amplification Kit for the Illumina platform (Ambion).
|
| |
|
| Hybridization protocol |
Hybrization were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).
|
| Scan protocol |
Staining and scanning were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).
|
| Description |
replicate 3
|
| Data processing |
The data were filtered removing any probes with a detection p-value above 0.01 for all the samples in the set. This remove any probes not detected at all in the set. It has been done before transformation via variance stabilisation and normalisation in order to reduce the noise of the set before normalisation. The data were then transformed using VST (Variance Stabilizing Transform) and normalised by quantile normalisation.
|
| |
|
| Submission date |
Sep 28, 2011 |
| Last update date |
Oct 24, 2011 |
| Contact name |
Jose Silva |
| E-mail(s) |
jcs64@cam.ac.uk
|
| Organization name |
Wellcome Trust Centre for Stem Cell Research
|
| Department |
Biochemistry
|
| Lab |
Jose Silva
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 1QR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE32464 |
Global gene expression analysis in murine iPS cells derived with mouse and human Nanog orthologs |
| GSE32715 |
Global gene expression analysis in murine iPS cells derived with Nanog orthologs |
|
