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Sample GSM2522875 Query DataSets for GSM2522875
Status Public on Jun 06, 2018
Title Normal_6454
Sample type RNA
Source name Normal sample from prostate cancer patient 6454
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 6454
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 36055
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 1.891337544
SNP_A-1967418 1.913871158
SNP_A-1969580 1.904817143
SNP_A-4263484 1.707507882
SNP_A-1978185 2.704577064
SNP_A-4264431 2.103375497
SNP_A-1980898 1.737180929
SNP_A-1983139 2.24963306
SNP_A-4265735 1.981197969
SNP_A-1995832 1.969120863
SNP_A-1995893 2.370801567
SNP_A-1997689 1.704019967
SNP_A-1997709 1.922354304
SNP_A-1997896 1.693273718
SNP_A-1997922 2.089073028
SNP_A-2000230 1.983758231
SNP_A-2000332 2.339153742
SNP_A-2000337 2.238289941
SNP_A-2000342 1.872842379
SNP_A-4268173 1.952723814

Total number of rows: 905422

Table truncated, full table size 22875 Kbytes.

Supplementary file Size Download File type/resource
GSM2522875_36055.CEL.gz 27.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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