|
| 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
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B08_238200.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 |
|
