|
| Status |
Public on Apr 10, 2010 |
| Title |
Virgin, MaSC-enriched, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
FACS sorted mammary cell subpopulation
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
cell subpopulation: MaSc-enriched
pregnancy status: Virgin
beadchip barcode: 4936586022
beadchip section: B
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the MaSC-enriched population (CD29hiCD24+) and luminal cells population (CD29loCD24+) sorted at > 90% purity using the miRNeasy Mini kit (Qiagen) and the DNA-free Kit (Ambion). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.
|
| Label |
Cy3
|
| Label protocol |
Up to 250 ng of RNA was labelled with the standard Total Prep RNA amplification kit (Ambion)
|
| |
|
| Hybridization protocol |
Complementary RNA (1.5 µg) was hybridised to Illumina MouseWG-6 V2 BeadChips.
|
| Scan protocol |
After washing, chips were with Cy3 and scanned in an Illumina BeadArray Reader.
|
| Description |
Virgin, MaSC-enriched, replicate 3
|
| Data processing |
Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normalized using the neqc function (which does normexp background correction and quantile normalisation using control probes) with offset 50.
|
| |
|
| Submission date |
Feb 18, 2010 |
| Last update date |
Mar 30, 2010 |
| 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) |
| GSE20402 |
Mouse mammary epithelial cell subpopulations from pregnant and virgin mice |
| GSE22446 |
Control of mammary stem cell function by steroid hormone signalling. |
|
