Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 15
Release date: Sep 24 2015
Last update date: Dec 3 2015
Access: Public
Diseases: Neoplasms, Rectal Neoplasms, Intraabdominal Infections
Computational protocol: XSTK, BWA, SAMtools, SnpEff, ANNOVAR, SciClone, dbSNP
Dataset link Intra-tumor Genetic Heterogeneity in Rectal Canger

Experimental Protocol


Affymetrix OncoScan V3 arrays were run on all tumor samples. The OncoScan array platform consists of a set of 217k probes designed specifically for profiling tumors. The overall resolution of the assay for detecting copy number change generates data at 50-100kb resolution across a set of 891 cancer genes, and 300-400kb across the rest of the genome. Raw array florescence intensity data generated on the Affymetrix scanners in the form of CEL files were loaded into the OncoScan Console software v.1.1.0 (Affymetrix, Santa Clara, California). Quality control statistics as well as integrated OSCHP files were generated by OncoScan Console. The standard Affymetrix reference control file for OncoScan data was used for processing the arrays.

Repositories


GEO

GSE73365

ArrayExpress

E-GEOD-73365

BioProject

PRJNA296805

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Contact


Ana Grant
Ana Rodrigues Grant

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