|
| Status |
Public on Sep 30, 2012 |
| Title |
Premalignant preB cell_Smchd1 wildtype_Rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Premalignant preB cell, Smchd1 wildtype
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Smchd1 wildtype
cell type: Premalignant preB cell
beadchip barcode: 7800238011
beadchip section: A
|
| Treatment protocol |
Tissue was stored in in buffer RLT (Qiagen) at -80 degrees until processing with an RNEasy kit.
|
| Growth protocol |
All samples were harvested fresh from mice and purified by cell sorting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
Cy3
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
WT 1
|
| Data processing |
Un-normalized summary probe profiles were exported from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected, normalized and log2-transformed with offset 16.
|
| |
|
| Submission date |
Sep 14, 2012 |
| Last update date |
Sep 30, 2012 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE40881 |
The effect on gene expression of Smchd1 deletion in premalignant pre-B cells |
| GSE40992 |
The effect on gene expression of Smchd1 deletion in various cell types |
|
