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Sample GSM720211 Query DataSets for GSM720211
Status Public on May 05, 2011
Title Case 3 Original
Sample type genomic
Source name renal cell carcinoma
Organism Homo sapiens
Characteristics disease state: renal cell carcinoma (RCC)
case: 3
tissue: original RCC
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 O3
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 0.025029
CN_000265 -0.254117
CN_000274 -0.111695
CN_000281 0.109026
CN_000285 0.039840
CN_000288 -0.111695
CN_000292 -0.083141
CN_000296 -0.079326
CN_000297 -0.117944
CN_000306 -0.261016
CN_000307 0.243669
CN_000310 0.115699
CN_000329 0.440421
CN_000331 0.364572
CN_000347 -0.599462
CN_000348 0.316146
CN_000370 0.239398
CN_000381 -0.122648
CN_000385 0.048934
CN_000401 -0.096190

Total number of rows: 1851810

Table truncated, full table size 39023 Kbytes.

Supplementary file Size Download File type/resource
GSM720211.CEL.gz 32.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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