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Sample GSM2522857 Query DataSets for GSM2522857
Status Public on Jun 06, 2018
Title Normal_2621
Sample type RNA
Source name Normal sample from prostate cancer patient 2621
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 2621
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 36075
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 1.565356259
SNP_A-1967418 1.857084143
SNP_A-1969580 2.093010858
SNP_A-4263484 1.978554869
SNP_A-1978185 1.382007537
SNP_A-4264431 1.649433071
SNP_A-1980898 1.761925736
SNP_A-1983139 1.649408886
SNP_A-4265735 1.542420587
SNP_A-1995832 1.659538733
SNP_A-1995893 1.593138402
SNP_A-1997689 2.095142386
SNP_A-1997709 1.938638877
SNP_A-1997896 2.17242041
SNP_A-1997922 1.819310545
SNP_A-2000230 2.426367177
SNP_A-2000332 1.863028968
SNP_A-2000337 1.669454958
SNP_A-2000342 2.040237505
SNP_A-4268173 1.410744937

Total number of rows: 905422

Table truncated, full table size 22872 Kbytes.

Supplementary file Size Download File type/resource
GSM2522857_36075.CEL.gz 28.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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