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Sample GSM796389 Query DataSets for GSM796389
Status Public on Feb 01, 2012
Title Normal Breast Sample [ATM_33]
Sample type RNA
Source name Normal Breast Sample
Organism Homo sapiens
Characteristics tissue: breast
gender: female
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from all samples using Qiazol (Invitrogen, Carlsbad, CA, USA) following manufacturer's instructions. The RNA was subsequently treated with DNaseI and repurified using acidic phenol-chlorophorm, and ethanol precipitation. DNA and RNA integrity were checked using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Data processing The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.
Submission date Sep 14, 2011
Last update date Jan 26, 2015
Contact name Ana Teresa Maia
Organization name University of Cambridge
Department Department of Oncology
Lab Cambridge Research Institute
Street address Robinson Way
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0RE
Country United Kingdom
Platform ID GPL6947
Series (2)
GSE32124 Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers [expression data]
GSE32259 Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers
Reanalyzed by GSE62502
Reanalyzed by GSE65314

Data table header descriptions
VALUE log base 2 transformed and quantile normalized

Data table
ILMN_2416019 7.075161074
ILMN_2415979 12.54851872
ILMN_2415949 9.035984585
ILMN_2415926 8.902491685
ILMN_2415911 8.576753052
ILMN_2415898 8.52071733
ILMN_2415826 7.425785525
ILMN_2415786 8.005759528
ILMN_2415776 7.561377281
ILMN_2415748 11.1806149
ILMN_2415722 14.37568846
ILMN_2415653 7.189126123
ILMN_2415650 7.413278866
ILMN_2415634 7.019704187
ILMN_2415617 7.306209562
ILMN_2415583 7.750831771
ILMN_2415572 7.484760471
ILMN_2415536 8.071611319
ILMN_2415529 8.9148335
ILMN_2415474 7.311836505

Total number of rows: 48803

Table truncated, full table size 1186 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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