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Sample GSM2522935 Query DataSets for GSM2522935
Status Public on Jun 06, 2018
Title Cancer_8418
Sample type RNA
 
Source name Cancer sample from prostate cancer patient 8418
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8418
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 36313
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 2.790196853
SNP_A-1967418 2.279750073
SNP_A-1969580 1.79391281
SNP_A-4263484 1.943321586
SNP_A-1978185 3.089344913
SNP_A-4264431 2.059673989
SNP_A-1980898 1.909496359
SNP_A-1983139 2.314134763
SNP_A-4265735 2.471890371
SNP_A-1995832 1.657311132
SNP_A-1995893 1.539680284
SNP_A-1997689 2.857361635
SNP_A-1997709 2.006668142
SNP_A-1997896 2.061413948
SNP_A-1997922 2.173559131
SNP_A-2000230 2.217398358
SNP_A-2000332 2.077218497
SNP_A-2000337 1.913041228
SNP_A-2000342 2.432786627
SNP_A-4268173 2.194914104

Total number of rows: 905422

Table truncated, full table size 22874 Kbytes.




Supplementary file Size Download File type/resource
GSM2522935_36313.CEL.gz 27.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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