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Sample GSM796377 Query DataSets for GSM796377
Status Public on Feb 01, 2012
Title Normal Breast Sample [ATM_21]
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 7.422314113
ILMN_2415979 12.01624868
ILMN_2415949 9.148428987
ILMN_2415926 9.185633361
ILMN_2415911 8.517140586
ILMN_2415898 8.125669026
ILMN_2415826 7.377722034
ILMN_2415786 8.871154061
ILMN_2415776 7.535006981
ILMN_2415748 11.29889582
ILMN_2415722 13.94283283
ILMN_2415653 6.915478543
ILMN_2415650 7.220936691
ILMN_2415634 7.275177608
ILMN_2415617 7.495701398
ILMN_2415583 7.664937685
ILMN_2415572 7.603590027
ILMN_2415536 8.202490008
ILMN_2415529 9.173897466
ILMN_2415474 7.530095061

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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