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Sample GSM2522866 Query DataSets for GSM2522866
Status Public on Jun 06, 2018
Title Cancer_4733
Sample type RNA
 
Source name Cancer 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: 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 36048
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 1.748568393
SNP_A-1967418 1.036201843
SNP_A-1969580 1.486991518
SNP_A-4263484 1.732990419
SNP_A-1978185 1.295527805
SNP_A-4264431 1.553470222
SNP_A-1980898 2.115434086
SNP_A-1983139 2.101052565
SNP_A-4265735 1.825801075
SNP_A-1995832 1.621898462
SNP_A-1995893 1.067321408
SNP_A-1997689 2.021396592
SNP_A-1997709 1.942528088
SNP_A-1997896 1.963020041
SNP_A-1997922 2.445044605
SNP_A-2000230 1.9581717
SNP_A-2000332 1.959111073
SNP_A-2000337 1.596171785
SNP_A-2000342 1.658193862
SNP_A-4268173 1.691635022

Total number of rows: 905422

Table truncated, full table size 22872 Kbytes.




Supplementary file Size Download File type/resource
GSM2522866_36048.CEL.gz 28.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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