Resource: Illumina microarray data sets

Data sets from NCBI's Gene Expression Omnibus (GEO)

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  URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=illumina

GSE11976: Segmentation-based detection of allelic imbalance and LOH in cancer cells using whole genome SNP arrays
Chip type(s): HumanCNV370v1
Description: The proposed segmentation strategy detects allelic imbalance originating from DNA copy number gain, loss or copy neutral events. Here we use Illumina 317K, 370K and 550K and Affymetrix 250K whole-genome single-nucleotide polymorphism arrays hybridized with tumor samples (breast, colon, leukemia, and urothelial) to evaluate the segmentation strategy against several other reported methods. The data sets include a simulated dilution series, an experimental dilution series of a breast cancer cell line as well as paired tumor-normal samples. This GEO series include the 12 sample experimental dilution series of the HCC1395 breast cancer cell line (CRL-2324: www.atcc.org) and 4 paired urothelial tumor-normal samples, all hybridized on Illumina HumanCNV 370k BeadChips.
Reference(s): Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A et al. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol 2008;9(9):R136.
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976
URL2: http://baseplugins.thep.lu.se/wiki/se.lu.onk.BAFsegmentation