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Sample GSM2522876 Query DataSets for GSM2522876
Status Public on Jun 06, 2018
Title Cancer_6539
Sample type RNA
 
Source name Cancer sample from prostate cancer patient 6539
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 6539
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 36245
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 1.624074234
SNP_A-1967418 2.713435039
SNP_A-1969580 2.044903287
SNP_A-4263484 2.427559409
SNP_A-1978185 3.106579738
SNP_A-4264431 2.055625559
SNP_A-1980898 2.066950384
SNP_A-1983139 1.665534311
SNP_A-4265735 1.04766749
SNP_A-1995832 1.496923905
SNP_A-1995893 2.085524143
SNP_A-1997689 2.407683472
SNP_A-1997709 2.114242367
SNP_A-1997896 1.700955819
SNP_A-1997922 1.83697505
SNP_A-2000230 1.945455226
SNP_A-2000332 2.137162758
SNP_A-2000337 1.901367472
SNP_A-2000342 1.946844828
SNP_A-4268173 2.034315148

Total number of rows: 905422

Table truncated, full table size 22872 Kbytes.




Supplementary file Size Download File type/resource
GSM2522876_36245.CEL.gz 28.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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