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Status |
Public on Jul 24, 2012 |
Title |
UZHRCC186_renal_tissue_reference_genomic |
Sample type |
genomic |
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Source name |
normal renal tissue
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Organism |
Homo sapiens |
Characteristics |
sample type: reference gender: male grade: NA stage: NA icd-o 3 code: NA icd-o 3 diagnosis text: NA organ site: kidney tissue type: normal renal tissue study cluster id: NA
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Treatment protocol |
untreated tissue biopsies and cell lines
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Growth protocol |
NA
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Extracted molecule |
genomic DNA |
Extraction protocol |
standard genomic DNA extraction methods
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Label |
biotin
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Label protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
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Hybridization protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
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Scan protocol |
Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).
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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.
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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.
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Submission date |
Jan 20, 2010 |
Last update date |
Jul 25, 2012 |
Contact name |
Michael Baudis |
E-mail(s) |
mbaudis@gmail.com
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Organization name |
University of Zurich
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Department |
Institute of Molecular Life Sciences
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Street address |
Winterthurerstrasse 190
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City |
Zurich |
ZIP/Postal code |
8057 |
Country |
Switzerland |
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Platform ID |
GPL6801 |
Series (1) |
GSE19949 |
Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome |
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