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Sample GSM2522870 Query DataSets for GSM2522870
Status Public on Jun 06, 2018
Title Cancer_4958
Sample type RNA
Source name Cancer sample from prostate cancer patient 4958
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 4958
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 36246
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 2.176720468
SNP_A-1967418 2.922968731
SNP_A-1969580 2.184227283
SNP_A-4263484 2.13205857
SNP_A-1978185 2.001534398
SNP_A-4264431 1.822684979
SNP_A-1980898 1.984317533
SNP_A-1983139 1.886865542
SNP_A-4265735 2.21590033
SNP_A-1995832 1.729615651
SNP_A-1995893 2.625814842
SNP_A-1997689 1.953184976
SNP_A-1997709 2.08939242
SNP_A-1997896 1.951389191
SNP_A-1997922 2.158247218
SNP_A-2000230 1.967503939
SNP_A-2000332 1.780883128
SNP_A-2000337 2.374045843
SNP_A-2000342 1.986437627
SNP_A-4268173 2.207886238

Total number of rows: 905422

Table truncated, full table size 22874 Kbytes.

Supplementary file Size Download File type/resource
GSM2522870_36246.CEL.gz 27.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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