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Sample GSM2522924 Query DataSets for GSM2522924
Status Public on Jun 06, 2018
Title Normal_8220
Sample type RNA
Source name Normal sample from prostate cancer patient 8220
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8220
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 36089
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 2.524653825
SNP_A-1967418 2.329947949
SNP_A-1969580 2.124881326
SNP_A-4263484 1.631370005
SNP_A-1978185 1.805243423
SNP_A-4264431 2.259396542
SNP_A-1980898 2.547836661
SNP_A-1983139 1.550864618
SNP_A-4265735 1.932001621
SNP_A-1995832 1.372178284
SNP_A-1995893 2.189803772
SNP_A-1997689 1.976861289
SNP_A-1997709 1.722231591
SNP_A-1997896 2.608116489
SNP_A-1997922 2.29904882
SNP_A-2000230 2.184083222
SNP_A-2000332 1.708727999
SNP_A-2000337 1.867053845
SNP_A-2000342 1.999059321
SNP_A-4268173 2.357885946

Total number of rows: 905422

Table truncated, full table size 22874 Kbytes.

Supplementary file Size Download File type/resource
GSM2522924_36089.CEL.gz 27.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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