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Sample GSM498900 Query DataSets for GSM498900
Status Public on Jul 24, 2012
Title UZHRCC163_renal_tissue_reference_genomic
Sample type genomic
 
Source name normal renal tissue
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
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

Supplementary file Size Download File type/resource
GSM498900_UZHRCC163,GenomeWideSNP_6,CN,raw.csv.gz 26.8 Mb (ftp)(http) CSV
GSM498900_UZHRCC163,GenomeWideSNP_6,segments.csv.gz 20.9 Kb (ftp)(http) CSV
GSM498900_UZHRCC163,GenomeWideSNP_6.CEL.gz 32.9 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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