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Sample GSM2522950 Query DataSets for GSM2522950
Status Public on Jun 06, 2018
Title Normal_8867
Sample type RNA
 
Source name Normal sample from prostate cancer patient 8867
Organism Homo sapiens
Characteristics subject status: prostate cancer patient
subject id: patient 8867
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 36101
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 2.823731352
SNP_A-1967418 2.158266002
SNP_A-1969580 1.630565344
SNP_A-4263484 2.033491648
SNP_A-1978185 4.127814113
SNP_A-4264431 1.738498533
SNP_A-1980898 1.884526169
SNP_A-1983139 2.914806354
SNP_A-4265735 2.714299274
SNP_A-1995832 2.089465607
SNP_A-1995893 2.642846545
SNP_A-1997689 2.143120623
SNP_A-1997709 2.116001664
SNP_A-1997896 1.870836892
SNP_A-1997922 2.287751925
SNP_A-2000230 1.892051435
SNP_A-2000332 2.513695372
SNP_A-2000337 1.806061767
SNP_A-2000342 2.6281657
SNP_A-4268173 1.972346795

Total number of rows: 905422

Table truncated, full table size 22873 Kbytes.




Supplementary file Size Download File type/resource
GSM2522950_36101.CEL.gz 27.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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