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Sample GSM2522955 Query DataSets for GSM2522955
Status Public on Jun 06, 2018
Title Cancer_9014
Sample type RNA
Source name Cancer sample from prostate cancer patient 9014
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 9014
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 36102
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 2.476682917
SNP_A-1967418 1.238541282
SNP_A-1969580 2.167552778
SNP_A-4263484 3.445677136
SNP_A-1978185 0
SNP_A-4264431 1.40382831
SNP_A-1980898 1.261046188
SNP_A-1983139 3.410636784
SNP_A-4265735 3.000874201
SNP_A-1995832 3.024338377
SNP_A-1995893 2.471858525
SNP_A-1997689 2.084773807
SNP_A-1997709 2.522192915
SNP_A-1997896 1.305055882
SNP_A-1997922 0.955474698
SNP_A-2000230 1.427403314
SNP_A-2000332 2.180511537
SNP_A-2000337 2.539814708
SNP_A-2000342 2.139321396
SNP_A-4268173 1.087174139

Total number of rows: 905422

Table truncated, full table size 22788 Kbytes.

Supplementary file Size Download File type/resource
GSM2522955_36102.CEL.gz 29.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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