|
| Status |
Public on Jan 23, 2010 |
| Title |
pNSC rep2 |
| Sample type |
RNA |
| |
|
| Source name |
parthenogenetic NSC
|
| Organism |
Mus musculus |
| Characteristics |
gender: parthenogenetic
cell type: neural stem cell
|
| 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 |
Specifically, 400 ng of total RNA per sample was used as input into a linear amplification protocol for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions, which involved synthesis of T7-linked double-stranded cDNA and 10-12 hrs of in-vitro transcription (IVT) incorporating biotin-labelled nucleotides.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol. Purified and labelled cRNA was then 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). Samples were exclusively hybridized as biological replicates.
|
| Scan protocol |
Standard Illumina scanning protocol. Scanned using the iScan reader (Illumina) and accompanying software.
|
| Description |
pNSC: Mouse parthenogenetic NSC (Neural Stem Cell).
Replicate 2.
|
| 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 |
Apr 06, 2009 |
| 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 |
GPL6885 |
| Series (1) |
| GSE15561 |
Generation of parthenogenetic iPS cells from parthenogenetic neural stem cell |
|
