|
| Status |
Public on Jul 24, 2012 |
| Title |
UZHRCC019_renal_tissue_neoplasia_genomic |
| Sample type |
genomic |
| |
|
| Source name |
renal cell carcinoma [clear cell RCC]
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: neoplasia
gender: male
grade: 3
stage: 3
icd-o 3 code: 8310/3
icd-o 3 diagnosis text: clear cell renal cell carcinoma
organ site: kidney
tissue type: renal cell carcinoma [clear cell RCC]
study cluster id: A
|
| Treatment protocol |
untreated tissue biopsies and cell lines
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard genomic DNA extraction methods
|
| Label |
biotin
|
| Label protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
|
| |
|
| Hybridization protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
|
| Scan protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
|
| Description |
Per case segmentation files (... segments.csv) and raw copy number files after aroma.affymetrix normalization (... ,CN,raw.csv) are provided as tab-delimited text files. Probes are mapped by their position in genome build 36 / HG18. Probes are ordered according to their linear position on the Golden Path.
|
| Data processing |
CEL files were processed with R using the aroma.affymetrix package. Background correction was done using the CRMAv2 method (Bengtstroem et al.). Segmentation was done using the circular binary segmentation (CBS) method. Post-segmentation thresholding & visualization were done using tools implemented through the Progenetix project (www.progenetix.net). For detection of small regional CNAs, adaptive thresholding was used, with a 100-300kb size filter and +/-0.13-0.15 thresholds on the segmentation data.
|
| |
|
| Submission date |
Jan 20, 2010 |
| Last update date |
Jul 25, 2012 |
| Contact name |
Michael Baudis |
| E-mail(s) |
mbaudis@gmail.com
|
| Organization name |
University of Zurich
|
| Department |
Institute of Molecular Life Sciences
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE19949 |
Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome |
|
