GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2522846 Query DataSets for GSM2522846
Status Public on Jun 06, 2018
Title Cancer_1356
Sample type RNA
Source name Cancer sample from prostate cancer patient 1356
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 1356
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 36106
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 1.86383551
SNP_A-1967418 1.839428099
SNP_A-1969580 2.136504422
SNP_A-4263484 2.131079367
SNP_A-1978185 3.15412485
SNP_A-4264431 2.481565766
SNP_A-1980898 2.198533126
SNP_A-1983139 1.889498556
SNP_A-4265735 2.208201489
SNP_A-1995832 2.040859306
SNP_A-1995893 1.794462135
SNP_A-1997689 1.992645498
SNP_A-1997709 2.750281912
SNP_A-1997896 1.948827279
SNP_A-1997922 2.351617867
SNP_A-2000230 2.124354962
SNP_A-2000332 1.950808812
SNP_A-2000337 2.0887932
SNP_A-2000342 2.178149722
SNP_A-4268173 2.019729579

Total number of rows: 905422

Table truncated, full table size 22872 Kbytes.

Supplementary file Size Download File type/resource
GSM2522846_36106.CEL.gz 28.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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