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Sample GSM511129 Query DataSets for GSM511129
Status Public on Apr 10, 2010
Title 12.5 dP, MaSC-enriched, replicate 1
Sample type RNA
 
Source name FACS sorted mammary cell subpopulation
Organism Mus musculus
Characteristics gender: female
cell subpopulation: MaSc-enriched
pregnancy status: Pregnant
beadchip barcode: 4936586023
beadchip section: C
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 12.5 dP, MaSC-enriched, replicate 1
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.

Data table header descriptions
ID_REF
VALUE limma-software normalized log2-intensity values

Data table
ID_REF VALUE
ILMN_2417611 5.911021813
ILMN_2762289 5.92329984
ILMN_2896528 12.58511475
ILMN_2721178 10.09637424
ILMN_2458837 5.913531989
ILMN_3033922 10.53259094
ILMN_3092673 12.77281497
ILMN_1230777 12.26317021
ILMN_1246069 11.52137181
ILMN_1232042 5.868575293
ILMN_1243193 9.233273485
ILMN_2524361 6.017265376
ILMN_1242440 5.904172282
ILMN_1233188 8.742171751
ILMN_2543688 11.38571906
ILMN_1259789 6.172570638
ILMN_2816356 7.031783914
ILMN_1224596 8.340987503
ILMN_1233643 6.004587813
ILMN_2808939 10.43806987

Total number of rows: 45281

Table truncated, full table size 1100 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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