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Sample GSM2522954 Query DataSets for GSM2522954
Status Public on Jun 06, 2018
Title Normal_8941
Sample type RNA
Source name Normal sample from prostate cancer patient 8941
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8941
ethnic background: African American (AA)
tissue type: normal; matched benign prostate tissue
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 36069
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 2.358552861
SNP_A-1967418 2.409657425
SNP_A-1969580 1.888478475
SNP_A-4263484 2.061327821
SNP_A-1978185 2.679183597
SNP_A-4264431 2.249320024
SNP_A-1980898 1.956139995
SNP_A-1983139 2.285467339
SNP_A-4265735 2.495214586
SNP_A-1995832 2.210713881
SNP_A-1995893 2.200045247
SNP_A-1997689 2.54138369
SNP_A-1997709 1.909283302
SNP_A-1997896 1.919933203
SNP_A-1997922 2.009426462
SNP_A-2000230 2.368912523
SNP_A-2000332 1.730929577
SNP_A-2000337 2.564415587
SNP_A-2000342 1.708415163
SNP_A-4268173 2.097017476

Total number of rows: 905422

Table truncated, full table size 22876 Kbytes.

Supplementary file Size Download File type/resource
GSM2522954_36069.CEL.gz 27.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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