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Series GSE17359 Query DataSets for GSE17359
Status Public on Feb 01, 2010
Title Affymetrix SNP array data for melanoma short-term cultures and cell lines
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary SNP arrays were used to derive copy number estimates and identify amplifications and deletions in melanomas
These copy number breakpoints were compared to gene fusions identified by second generation sequencing of cDNA
Overall design Affymetrix SNP 6.0 array hybridizations were performed for 3 melanomas and 15 normal diploid samples (in a batch of 96 total samples encompassing multiple studies).

Further normalization performed to convert signal intensities (see Sample data tables) into copy number log2 ratios for each probeset (see supplementary file at the foot of this record) using the 5 most similar HapMap normals, as described by the Cancer Genome Atlast Research Network, Nature (2008), 455:1061-1068.
Contributor(s) Berger MF, Garraway LA
Citation(s) 20179022
Submission date Jul 27, 2009
Last update date Nov 27, 2018
Contact name Michael Berger
Organization name The Broad Instititute
Department Cancer Program
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (18)
GSM433916 melanoma short-term culture M000921
GSM433917 melanoma short-term culture M990802
GSM433918 melanoma cell line 501Mel
This SubSeries is part of SuperSeries:
GSE17593 Melanoma short-term cultures and cell lines: expression profiling and CNV analyses
BioProject PRJNA123405

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
GSE17359_RAW.tar 534.8 Mb (http)(custom) TAR (of CEL)
GSE17359_affy_snp_ratios_matrix.txt.gz 144.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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