|
| Status |
Public on Nov 25, 2009 |
| Title |
iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 6 |
| Sample type |
RNA |
| |
|
| Source name |
iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 6
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iPS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from repective clones or cell cultures were harvested and then washed with PBS, trypsinised, resuspended in RNAlater and stored at -20°C. Total RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.
|
| Label |
Biotin
|
| Label protocol |
500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).
|
| |
|
| Hybridization protocol |
750ng of each labelled cRNA sample was hybridized to MouseRef-8 v2 Expression BeadChip microarrays (Illumina) according to manufacturer specifications.
|
| Scan protocol |
Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.
|
| Description |
Clone 6
|
| Data processing |
The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006).
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.
|
| |
|
| Submission date |
Nov 24, 2009 |
| Last update date |
Nov 24, 2009 |
| Contact name |
Henry Yang |
| E-mail(s) |
henry_yang@immunol.a-star.edu.sg
|
| Organization name |
SIgN
|
| Department |
Bioinformatics Group
|
| Street address |
8A Biomedical Grove
|
| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6103 |
| Series (1) |
| GSE19164 |
Tbx3 improves the germ-line competency of induced pluripotent stem cells |
|
