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Sample GSM2522867 Query DataSets for GSM2522867
Status Public on Jun 06, 2018
Title Normal_4733
Sample type RNA
 
Source name Normal sample from prostate cancer patient 4733
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 4733
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 36049
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
E-mail(s) creighto@bcm.tmc.edu
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
ID_REF
VALUE Copy number

Data table
ID_REF VALUE
SNP_A-2131660 1.830315856
SNP_A-1967418 1.238541282
SNP_A-1969580 2.287179708
SNP_A-4263484 1.915829919
SNP_A-1978185 1.662598611
SNP_A-4264431 1.758740684
SNP_A-1980898 1.98964597
SNP_A-1983139 2.074178563
SNP_A-4265735 1.974026192
SNP_A-1995832 1.78695673
SNP_A-1995893 1.648464717
SNP_A-1997689 1.953518401
SNP_A-1997709 2.868634278
SNP_A-1997896 2.620826386
SNP_A-1997922 1.89364026
SNP_A-2000230 1.723612984
SNP_A-2000332 1.816217778
SNP_A-2000337 1.892664188
SNP_A-2000342 2.01275767
SNP_A-4268173 2.152252106

Total number of rows: 905422

Table truncated, full table size 22866 Kbytes.




Supplementary file Size Download File type/resource
GSM2522867_36049.CEL.gz 28.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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