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Sample GSM511120 Query DataSets for GSM511120
Status Public on Apr 10, 2010
Title Control, Luminal, technical replicate of replicate 1
Sample type RNA
 
Source name FACS sorted mammary cell subpopulation
Organism Mus musculus
Characteristics gender: female
cell subpopulation: Luminal
mouse type: control
mouse pool (biological replicate): 1
beadchip barcode: 5022532011
beadchip section: E
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 Control, Luminal, technical replicate of 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)
GSE20401 Mammary epithelial cell subpopulations from control and ovariectomized mice
GSE22446 Control of mammary stem cell function by steroid hormone signalling.

Data table header descriptions
ID_REF
VALUE limma computed log2-expression values

Data table
ID_REF VALUE
ILMN_2417611 5.993359526
ILMN_2762289 6.109643954
ILMN_2896528 12.61508294
ILMN_2721178 10.25008782
ILMN_2458837 5.991548502
ILMN_3033922 11.54241794
ILMN_3092673 13.39905164
ILMN_1230777 12.86363243
ILMN_1246069 11.36880502
ILMN_1232042 5.925580905
ILMN_1243193 11.24087909
ILMN_2524361 6.260759872
ILMN_1242440 5.9854375
ILMN_1233188 6.053690358
ILMN_2543688 6.79407681
ILMN_1259789 6.701443862
ILMN_2816356 7.188008468
ILMN_1224596 7.975698537
ILMN_1233643 5.938464157
ILMN_2808939 10.31714562

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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