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Sample GSM2319910 Query DataSets for GSM2319910
Status Public on Aug 31, 2018
Title Breast cancer tissue [T149] copy number
Sample type genomic
 
Source name Breast tumor
Organism Homo sapiens
Characteristics tissue: Breast cancer tissue
cell type: Somatic cell fraction
population: Mexican hispanic
Extracted molecule genomic DNA
Extraction protocol DNA from peripheral blood lymphocytes was extracted with the QIAamp DNA Blood Maxi Kit (Qiagen, Valencia, CA), according to manufacturer’s instructions
Label biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was digested with NspI and StyI enzymes (New England Biolabs), ligated to the respective Affymetrix adapters using T4 DNA ligase (New England Biolabs) amplified (Clontech), purified using magnetic beads (Agencourt), labeled, fragmented, and hybridized to the arrays
Scan protocol As per manufacturer (Affymetrix)
Description Hybridized to SNP6 Affymetrix
Data processing Background correction and extraction of raw fluorescence intensity were performed with the Affymetrix Genotyping Console. To generate the copy number profiles we used the “Copy Number Inference” pipeline implemented in genepattern: (http://genepattern.broadinstitute.org/gp/pages/index.jsf). In brief, probe-level signal intensities from Affymetrix SNP6 (cel files) were normalized to a uniform brightness and merged to obtain values for each probe set using SNP File Creator. These intensities measurements were converted into a copy number call by the Copy Number Inference model. After reducing the noise by subtracting out the variation that is also seen within the normal samples (peripheral blood), the CBS segmentation algorithm identifies regions in the genome that have a uniform underlying copy number, creating a segmentation file. Finally, we identified the significantly somatic alterations with GISTIC using the cnv segmentation results.
Matched normalized SCNA and SNPs
 
Submission date Sep 17, 2016
Last update date Aug 31, 2018
Contact name Sandra Lorena Romero-Cordoba
E-mail(s) sromero_cordoba@hotmail.com
Organization name National Instute of Genomic Medicine
Department Cancer Genomics
Street address Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.
City Mexico
State/province Mexico
ZIP/Postal code 14610
Country Mexico
 
Platform ID GPL6801
Series (2)
GSE87048 Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [copy number]
GSE87049 Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women

Supplementary file Size Download File type/resource
GSM2319910_T149.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
GSM2319910_T149.birdseed-v2.chp.txt.gz 15.7 Mb (ftp)(http) TXT
GSM2319910_T149_LumB.CEL.gz 29.8 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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