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Sample GSM511128 Query DataSets for GSM511128
Status Public on Apr 10, 2010
Title 12.5 dP, luminal, replicate 3
Sample type RNA
 
Source name FACS sorted mammary cell subpopulation
Organism Mus musculus
Characteristics gender: female
cell subpopulation: luminal
pregnancy status: Pregnant
beadchip barcode: 4936586023
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 12.5 dP, luminal, 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.

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

Data table
ID_REF VALUE
ILMN_2417611 5.898525512
ILMN_2762289 5.909925218
ILMN_2896528 12.56334573
ILMN_2721178 10.3771507
ILMN_2458837 5.918993061
ILMN_3033922 10.10237205
ILMN_3092673 12.55861562
ILMN_1230777 12.13350412
ILMN_1246069 11.86837551
ILMN_1232042 5.87814369
ILMN_1243193 10.54035487
ILMN_2524361 6.080724037
ILMN_1242440 5.949378281
ILMN_1233188 6.035644005
ILMN_2543688 8.037577483
ILMN_1259789 6.307100443
ILMN_2816356 6.838653105
ILMN_1224596 8.473583372
ILMN_1233643 5.963773554
ILMN_2808939 10.56907424

Total number of rows: 45281

Table truncated, full table size 1099 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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