GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2522964 Query DataSets for GSM2522964
Status Public on Jun 06, 2018
Title Normal_9124
Sample type RNA
Source name Normal sample from prostate cancer patient 9124
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 9124
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 36121
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 2.217125779
SNP_A-1967418 1.649351657
SNP_A-1969580 2.419529623
SNP_A-4263484 1.445706092
SNP_A-1978185 1.132331901
SNP_A-4264431 1.887726432
SNP_A-1980898 2.225032845
SNP_A-1983139 1.582306247
SNP_A-4265735 2.037173685
SNP_A-1995832 2.376826056
SNP_A-1995893 2.066621124
SNP_A-1997689 1.517991792
SNP_A-1997709 2.460065052
SNP_A-1997896 2.556051701
SNP_A-1997922 1.6462837
SNP_A-2000230 1.335578036
SNP_A-2000332 2.502224787
SNP_A-2000337 1.879928538
SNP_A-2000342 1.455179047
SNP_A-4268173 2.578968753

Total number of rows: 905422

Table truncated, full table size 22865 Kbytes.

Supplementary file Size Download File type/resource
GSM2522964_36121.CEL.gz 28.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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