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Sample GSM2522925 Query DataSets for GSM2522925
Status Public on Jun 06, 2018
Title Cancer_8305
Sample type RNA
Source name Cancer sample from prostate cancer patient 8305
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8305
ethnic background: African American (AA)
tissue type: highly tumor-enriched primary prostate cancer (PCa)
Growth protocol Tissue samples were obtained from the Human Tissue Acquisition and Pathology Core of the Dan L. Duncan Cancer Center and were collected from fresh radical prostatectomy specimens after obtaining informed consent under an Institutional Review Board approved protocol. Cancer tissues include at least 70% tumor tissue and benign tissues were free of cancer on pathological examination.
Extracted molecule genomic DNA
Extraction protocol DNAs extracted using a Qiagen DNA/RNA mini kit following the manufacturer’s protocol.
Label biotin
Label protocol According to Affymetix protocol.
Hybridization protocol According to Affymetix protocol.
Scan protocol According to Affymetix protocol.
Description 36252
Data processing Copy number values are estimated total copy number (e.g. 2~wild-type). Additional analysis details are as follows: "We fit a linear model to the normalized intensities stratified by the diallic genotype call. The intercept and slope from the linear model are both SNP- and batch-specific. Raw total copy number were estimated using crlmm package in Bioconductor (R 3.0., Bioconductor 2.12), using the default settings. At allele k, marker i, sample j, and batch p, the estimate of allelespecific copy number is computed by subtracting the estimated background from the normalized intensity and scaling by the slope coefficient.
Submission date Mar 06, 2017
Last update date Jun 07, 2018
Contact name Chad Creighton
Organization name Baylor College of Medicine
Department Biostatistics, Ducan Cancer Center
Street address One Baylor Plaza, Mail Stop: BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platform ID GPL6801
Series (1)
GSE95726 Copy number profiling of prostate cancers from 40 African American patients

Data table header descriptions
VALUE Copy number

Data table
SNP_A-2131660 2.680496167
SNP_A-1967418 1.741324129
SNP_A-1969580 1.945224148
SNP_A-4263484 1.922527082
SNP_A-1978185 1.67760616
SNP_A-4264431 1.818117659
SNP_A-1980898 1.986584841
SNP_A-1983139 2.506672821
SNP_A-4265735 2.232185854
SNP_A-1995832 1.648400731
SNP_A-1995893 1.442020004
SNP_A-1997689 2.412923728
SNP_A-1997709 2.002296885
SNP_A-1997896 2.200885577
SNP_A-1997922 1.842808018
SNP_A-2000230 2.464115815
SNP_A-2000332 2.229741871
SNP_A-2000337 1.565264727
SNP_A-2000342 1.92908498
SNP_A-4268173 2.015230017

Total number of rows: 905422

Table truncated, full table size 22873 Kbytes.

Supplementary file Size Download File type/resource
GSM2522925_36252.CEL.gz 27.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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