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Sample GSM2522881 Query DataSets for GSM2522881
Status Public on Jun 06, 2018
Title Normal_6544
Sample type RNA
 
Source name Normal sample from prostate cancer patient 6544
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 6544
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 36316
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
E-mail(s) creighto@bcm.tmc.edu
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
ID_REF
VALUE Copy number

Data table
ID_REF VALUE
SNP_A-2131660 2.201519967
SNP_A-1967418 2.869519785
SNP_A-1969580 1.810247557
SNP_A-4263484 2.043805023
SNP_A-1978185 1.992764676
SNP_A-4264431 2.481785737
SNP_A-1980898 1.989488248
SNP_A-1983139 1.912295561
SNP_A-4265735 1.872857875
SNP_A-1995832 1.804332758
SNP_A-1995893 1.804839617
SNP_A-1997689 2.390633047
SNP_A-1997709 1.626450505
SNP_A-1997896 1.835850242
SNP_A-1997922 2.531773563
SNP_A-2000230 2.624313652
SNP_A-2000332 1.930512457
SNP_A-2000337 1.710969892
SNP_A-2000342 2.311446452
SNP_A-4268173 1.942172471

Total number of rows: 905422

Table truncated, full table size 22873 Kbytes.




Supplementary file Size Download File type/resource
GSM2522881_36316.CEL.gz 27.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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