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Sample GSM2500548 Query DataSets for GSM2500548
Status Public on Jun 09, 2017
Title ccRCC [G3_713]
Sample type genomic
 
Source name clear cell renal cell carcinoma tissue
Organism Homo sapiens
Characteristics tumour grading: G3
Treatment protocol None
Growth protocol Tissue samples were taken immediately after resection of the kidney and cryoconserved in liquid nitrogen.
Extracted molecule genomic DNA
Extraction protocol About 30 mg tissue was disrupted using mortar and pestle immersed in liquid nitrogen. Genomic DNA was extracted with the QIAamp® DNA Mini Kit (Qiagen, Hilden) according to the manufacturers protocol.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to Genome-Wide Human SNP 6.0 Array
Data processing The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotyping Console 4.2.0. and Birdseed algoritm and Affymetrix Copy Number Analysis Tool (CNAT) softwares using default values.
 
Submission date Feb 23, 2017
Last update date Jun 09, 2017
Contact name Dirk Koczan
E-mail(s) dirk.koczan@med.uni-rostock.de
Phone +493814945885
Organization name University of Rostock
Department Institute for Immunology
Street address Schillingallee 70
City Rostock
ZIP/Postal code 18057
Country Germany
 
Platform ID GPL6801
Series (1)
GSE95239 Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.023837 AA 2246.508545 863.082520
SNP_A-1967418 AB 0.012011 AB 462.587219 527.968018
SNP_A-1969580 BB 0.006317 BB 894.203735 3628.450439
SNP_A-4263484 BB 0.024967 BB 363.914764 1000.095886
SNP_A-1978185 AA 0.009819 AA 2287.277832 443.338715
SNP_A-4264431 AB 0.012772 AB 1069.307983 471.274353
SNP_A-1980898 AB 0.017696 AB 339.315338 279.836761
SNP_A-1983139 AA 0.014360 AA 305.834137 249.286880
SNP_A-4265735 AB 0.009335 AB 633.652039 559.376282
SNP_A-1995832 AB 0.005351 AB 1822.646606 1619.481201
SNP_A-1995893 AB 0.003530 AB 1571.049927 1803.326660
SNP_A-1997689 BB 0.004192 BB 665.779053 3317.992188
SNP_A-1997709 AA 0.037566 AA 1841.926392 462.587219
SNP_A-1997896 AB 0.034785 AB 519.449158 659.057983
SNP_A-1997922 AB 0.031785 AB 349.476959 377.390167
SNP_A-2000230 AA 0.005411 AA 1691.039917 1042.207764
SNP_A-2000332 AA 0.018350 AA 2451.788818 850.731018
SNP_A-2000337 AA 0.009574 AA 1178.756958 500.449615
SNP_A-2000342 AA 0.023171 AA 1949.889893 799.930664
SNP_A-4268173 AA 0.012173 AA 940.549988 321.153442

Total number of rows: 909622

Table truncated, full table size 46117 Kbytes.




Supplementary file Size Download File type/resource
GSM2500548_G3_713.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM2500548_G3_713.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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