Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 16
Release date: Sep 26 2011
Last update date: Jan 30 2015
Access: Public
Diseases: Chondrosarcoma, Neoplasms, Vertigo, Tooth Loss, Uniparental Disomy
Computational protocol: GenomeStudio, tQN, GEO
Dataset link Clonal evolution through loss of chromosomes and subsequent polyploidization in chondrosarcoma

Experimental Protocol


Tumor DNA was hybridized onto Illumina Human Omni-Quad v1.0 BeadChip or Human CNV370-Quad v3.0 BeadChip (Illumina, San Diego, CA, USA), following standard protocols supplied by the manufacturer. Data were extracted from the GenomeStudio software (Illumina), and subsequently normalized and segmented using thresholded quantile normalization (tQN) and BAFsegmentation, respectively (Staaf et al. Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics 2007, 8:382; Staaf et al. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol 2008, 9:R136). Base pair positions are indicated according to the NCBI build 36 (hg18).

Repositories


GEO

GSE25985

ArrayExpress

E-GEOD-25985

BioProject

PRJNA135413

Download


Dataset Statistics

info

Citations per year

Dataset publication