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Sample GSM720212 Query DataSets for GSM720212
Status Public on May 05, 2011
Title Case 3 Xenograft
Sample type genomic
 
Source name renal cell carcinoma
Organism Homo sapiens
Characteristics disease state: renal cell carcinoma (RCC)
case: 3
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 X3
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B07_238198.CEL
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 (http://genome.ucsc.edu). 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
E-mail(s) cgrisanzio@partners.org
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
ID_REF
VALUE signal intensities refer to copy number data

Data table
ID_REF VALUE
CN_000263 0.552869
CN_000265 -0.940645
CN_000274 -0.069452
CN_000281 0.891808
CN_000285 -0.498179
CN_000288 -0.456999
CN_000292 0.257614
CN_000296 0.722029
CN_000297 0.501821
CN_000306 0.018634
CN_000307 0.957915
CN_000310 0.100305
CN_000329 1.370722
CN_000331 0.809414
CN_000347 0.077927
CN_000348 -0.067183
CN_000370 -0.140030
CN_000381 0.182057
CN_000385 0.652601
CN_000401 -0.052147

Total number of rows: 1851810

Table truncated, full table size 39048 Kbytes.




Supplementary file Size Download File type/resource
GSM720212.CEL.gz 30.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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