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Series GSE29062 Query DataSets for GSE29062
Status Public on May 05, 2011
Title Orthotopic xenografts of RCC retain histological, immunophenotypic and genetic features of tumors in patients
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Development of a clinically relevant animal models of RCC for preclinical investigations.
For DNA copy number analysis, the Sty I (250K) SNP array of the 500K Human Mapping Array (Affymetrix) was used. Arrays were scanned by GeneChip Scanner 3000 7G. Probe-level signal intensities were normalized to a baseline array with median intensity using invariant set normalization and SNP-level signal intensities were obtained using a model-based (PM/MM) method.
Keywords: SNP array data, renal cell carcinoma
Overall design To ensure at least 70% contribution from tumor cells, enriched tumor areas from 10 original RCCs and 10 corresponding xenografts were isolated from 7 ┬Ám-thick tissue frozen sections using a fine needle with the aid of an optical microscope. DNA was then extracted using phenol chloroform
Contributor(s) Grisanzio C, Seeley A, Chang M, Collins M, Di Napoli A, Cheng S, Percy A, Beroukhim R, Signoretti S
Citation(s) 21710693
Submission date May 04, 2011
Last update date Nov 27, 2018
Contact name Chiara Grisanzio
Organization name DFCI
Department Medical Oncology
Street address 44 Binney Street
City Boston
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (20)
GSM720211 Case 3 Original
GSM720212 Case 3 Xenograft
GSM720213 Case 5 Original
BioProject PRJNA140243

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
GSE29062_RAW.tar 615.2 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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