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Series GSE13372 Query DataSets for GSE13372
Status Public on Nov 14, 2008
Title High-resolution mapping of copy-number alterations with massively parallel sequencing
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC).
We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays.
We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246

Keywords: disease state analysis
Overall design 21 replicates of HCC1143 (breast ductal carcinoma), 21 replicates of HCC1143BL (matched normal), 13 replicates of HCC1954 (breast ductal carcinoma), 11 replicates of HCC1954BL (matched normal), 1 replicate of NCI-H2347 (lung adenocarcinoma), 1 replicate of NCI-H2347BL (matched normal)
Web link
Contributor(s) Chiang DY, Getz G, Jaffe D, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES
Citation(s) 19043412
Submission date Oct 27, 2008
Last update date Nov 27, 2018
Contact name Derek Chiang
Organization name University of North Carolina
Department Department of Genetics
Street address UNC Lineberger Cancer Center, 450 West Drive, CB #7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7295
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (68)
GSM337641 HCC1143_GLEYS_A02
GSM337642 HCC1143_GLEYS_C06
GSM337643 HCC1143_GLEYS_C10
This SubSeries is part of SuperSeries:
GSE13373 Mapping of copy-number alterations with massively parallel sequencing
BioProject PRJNA113945

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13372_RAW.tar 2.0 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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