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Sample GSM2522850 Query DataSets for GSM2522850
Status Public on Jun 06, 2018
Title Cancer_1810
Sample type RNA
Source name Cancer sample from prostate cancer patient 1810
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 1810
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 36072
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 2.810094934
SNP_A-1967418 2.299290459
SNP_A-1969580 1.984771429
SNP_A-4263484 1.908891627
SNP_A-1978185 3.754743616
SNP_A-4264431 2.53873822
SNP_A-1980898 2.252798866
SNP_A-1983139 2.557343808
SNP_A-4265735 2.442430563
SNP_A-1995832 2.12493352
SNP_A-1995893 1.203333936
SNP_A-1997689 2.003672337
SNP_A-1997709 1.707172752
SNP_A-1997896 1.634890246
SNP_A-1997922 1.923981106
SNP_A-2000230 2.654694706
SNP_A-2000332 3.08840278
SNP_A-2000337 2.353890071
SNP_A-2000342 1.885464074
SNP_A-4268173 1.802894969

Total number of rows: 905422

Table truncated, full table size 22876 Kbytes.

Supplementary file Size Download File type/resource
GSM2522850_36072.CEL.gz 26.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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