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Sample GSM2522926 Query DataSets for GSM2522926
Status Public on Jun 06, 2018
Title Normal_8305
Sample type RNA
Source name Normal sample from prostate cancer patient 8305
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8305
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 36240
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 1.557587764
SNP_A-1967418 1.647143011
SNP_A-1969580 1.903957419
SNP_A-4263484 2.051465719
SNP_A-1978185 2.764000446
SNP_A-4264431 1.673723651
SNP_A-1980898 2.597567784
SNP_A-1983139 2.262245227
SNP_A-4265735 1.432274825
SNP_A-1995832 2.437682446
SNP_A-1995893 1.487058731
SNP_A-1997689 2.51850298
SNP_A-1997709 2.184222452
SNP_A-1997896 2.221968497
SNP_A-1997922 1.967331841
SNP_A-2000230 1.591518551
SNP_A-2000332 2.027695263
SNP_A-2000337 1.883591136
SNP_A-2000342 2.134163896
SNP_A-4268173 1.963006928

Total number of rows: 905422

Table truncated, full table size 22870 Kbytes.

Supplementary file Size Download File type/resource
GSM2522926_36240.CEL.gz 28.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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