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Sample GSM1815612 Query DataSets for GSM1815612
Status Public on Feb 09, 2017
Title Leukocyte HB705
Sample type genomic
 
Source name Leukocyte HB705
Organism Homo sapiens
Characteristics cell type: Leukocyte
patient: HB705
age: 60
Stage: T2cN0MX
gleason: 4+3=7
nomogram 5 years: 0.93
recurrence label: no
fast relapase label: nf
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using Qiagen blood DNA extraction kit.
Label Biotin
Label protocol The fragmented DNA was labeled with biotinylated nucleotides through terminal deoxynucleotide transferase for 4 hours at 37oC, following the manual provided by Affymetrix, Inc.
 
Hybridization protocol Two hundred fifty micrograms of fragmented DNA were hybridized with a pre-equilibrated Affymetrix chip SNP 6.0 at 50oC for 18 hours. Procedures of washing and scanning of SNP 6.0 chips followed the manuals provided by Affymetrix, Inc.
Scan protocol The hybridized chips were scanned by 7G Affymetrix scanner.
Description Affymetrix SNP 6.0
Data processing CEL files were analyzed with Genotyping Console for quality control analysis. Samples with QC call above 80% and QC contrast ratio above 0.4 were admitted into the analysis. To analyze CNV, CEL files were imported into Partek GenomeSuite 6.6 to generate copy number from raw intensity.
Each CEL file represents data from one patient. Deletion or amplification of genomes were analyzed by first limiting to the regions with p-value less than 0.001. The selected regions were subsequently filtered by limiting to the regions with at least 10 markers and 2 kb in size.
 
Submission date Jul 08, 2015
Last update date Feb 09, 2017
Contact name Shuchang Liu
E-mail(s) silvia.shuchang.liu@gmail.com
Organization name University of Pittsburgh
Street address 130 De Soto Street
City Pittsburgh
State/province Pennsylvania
ZIP/Postal code 15261
Country USA
 
Platform ID GPL6801
Series (1)
GSE70650 Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes

Supplementary file Size Download File type/resource
GSM1815612_Luo_SNP_082112_HB705_Blood.CEL.gz 29.1 Mb (ftp)(http) CEL
Processed data are available on Series record

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