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Sample GSM2522856 Query DataSets for GSM2522856
Status Public on Jun 06, 2018
Title Cancer_2621
Sample type RNA
Source name Cancer sample from prostate cancer patient 2621
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 2621
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 36074
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 2.066764173
SNP_A-1967418 1.472893357
SNP_A-1969580 1.634863961
SNP_A-4263484 1.679495142
SNP_A-1978185 1.90698434
SNP_A-4264431 1.753342777
SNP_A-1980898 1.850012895
SNP_A-1983139 1.79632943
SNP_A-4265735 1.363659432
SNP_A-1995832 1.42302356
SNP_A-1995893 2.021447145
SNP_A-1997689 1.790893299
SNP_A-1997709 1.325817986
SNP_A-1997896 1.553654119
SNP_A-1997922 1.665508905
SNP_A-2000230 1.53898419
SNP_A-2000332 1.65655429
SNP_A-2000337 2.396031905
SNP_A-2000342 1.851736945
SNP_A-4268173 1.650744468

Total number of rows: 905422

Table truncated, full table size 22873 Kbytes.

Supplementary file Size Download File type/resource
GSM2522856_36074.CEL.gz 27.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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