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Sample GSM2522915 Query DataSets for GSM2522915
Status Public on Jun 06, 2018
Title Cancer_7546
Sample type RNA
Source name Cancer sample from prostate cancer patient 7546
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 7546
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 36122
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 1.64595776
SNP_A-1967418 2.906308774
SNP_A-1969580 2.335503692
SNP_A-4263484 1.691216671
SNP_A-1978185 0.997263965
SNP_A-4264431 2.39949255
SNP_A-1980898 2.567167877
SNP_A-1983139 1.811928356
SNP_A-4265735 1.514483804
SNP_A-1995832 2.300934373
SNP_A-1995893 1.923748092
SNP_A-1997689 2.169654124
SNP_A-1997709 2.246024117
SNP_A-1997896 2.184667945
SNP_A-1997922 2.015192107
SNP_A-2000230 1.999500187
SNP_A-2000332 2.13721846
SNP_A-2000337 2.098262634
SNP_A-2000342 2.26640975
SNP_A-4268173 2.601095598

Total number of rows: 905422

Table truncated, full table size 22874 Kbytes.

Supplementary file Size Download File type/resource
GSM2522915_36122.CEL.gz 28.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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