GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2522860 Query DataSets for GSM2522860
Status Public on Jun 06, 2018
Title Cancer_3533
Sample type RNA
Source name Cancer sample from prostate cancer patient 3533
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 3533
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 36076
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 1.989291066
SNP_A-1967418 2.091095957
SNP_A-1969580 1.956400553
SNP_A-4263484 2.02922394
SNP_A-1978185 2.273817921
SNP_A-4264431 1.98140434
SNP_A-1980898 2.206633606
SNP_A-1983139 1.816046005
SNP_A-4265735 1.81688216
SNP_A-1995832 1.844225037
SNP_A-1995893 1.465112298
SNP_A-1997689 2.209468003
SNP_A-1997709 1.712653482
SNP_A-1997896 1.911049621
SNP_A-1997922 2.048070914
SNP_A-2000230 2.50459645
SNP_A-2000332 2.090595145
SNP_A-2000337 2.119358761
SNP_A-2000342 1.893496061
SNP_A-4268173 1.918601088

Total number of rows: 905422

Table truncated, full table size 22876 Kbytes.

Supplementary file Size Download File type/resource
GSM2522860_36076.CEL.gz 27.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap