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Sample GSM720218 Query DataSets for GSM720218
Status Public on May 05, 2011
Title Case 8 Xenograft
Sample type genomic
Source name renal cell carcinoma
Organism Homo sapiens
Characteristics disease state: renal cell carcinoma (RCC)
case: 8
tissue: xenograft
Treatment protocol Frozen tissue was needle-dissected, lysed in SDS, and purified using phenol/chloroform
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA was performed using SDS with proteinase K, followed by phenol/chloroform and ethanol precipitation
Label biotin
Label protocol Biotinylated DNA were prepared according to the standard Affymetrix protocol from 250 ng genomic DNA
Hybridization protocol Following fragmentation, 40 ug of cRNA were hybridized for 16 hr at 48C on GeneChip 250K StyI Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description X8
SNP array data from renal cell carcinoma
Data processing Probe-level signal intensities (i.e. copy number data) 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. Significant regions of copy-number variation were determined using the Genomic Identification of Significant Targets In Cancer (GISTIC) method. SN, gene, and cytogenetic band locations are based on the hg18 genome build ( For the comparison between the Euclidean distance distributions among profiles of different subgroups, p-values were calculated by permuting group labels.
Submission date May 04, 2011
Last update date May 05, 2011
Contact name Chiara Grisanzio
Organization name DFCI
Department Medical Oncology
Street address 44 Binney Street
City Boston
ZIP/Postal code 02115
Country USA
Platform ID GPL6801
Series (1)
GSE29062 Orthotopic xenografts of RCC retain histological, immunophenotypic and genetic features of tumors in patients

Data table header descriptions
VALUE signal intensities refer to copy number data

Data table
CN_000263 0.718964
CN_000265 -0.112475
CN_000274 -0.052147
CN_000281 1.091869
CN_000285 -0.755113
CN_000288 -0.497160
CN_000292 0.754460
CN_000296 0.325962
CN_000297 0.066950
CN_000306 -0.181149
CN_000307 0.345964
CN_000310 0.444137
CN_000329 1.229895
CN_000331 0.415218
CN_000347 1.308594
CN_000348 -1.125006
CN_000370 0.393416
CN_000381 0.285106
CN_000385 0.182057
CN_000401 0.541515

Total number of rows: 1851810

Table truncated, full table size 39083 Kbytes.

Supplementary file Size Download File type/resource
GSM720218.CEL.gz 30.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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