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Sample GSM2522880 Query DataSets for GSM2522880
Status Public on Jun 06, 2018
Title Cancer_6544
Sample type RNA
 
Source name Cancer 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: 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 36315
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 1.856973698
SNP_A-1967418 1.845559597
SNP_A-1969580 2.233339772
SNP_A-4263484 2.082205734
SNP_A-1978185 2.397968483
SNP_A-4264431 2.254907918
SNP_A-1980898 2.071914314
SNP_A-1983139 1.563406616
SNP_A-4265735 1.752149848
SNP_A-1995832 2.611598767
SNP_A-1995893 1.990620042
SNP_A-1997689 2.33348092
SNP_A-1997709 1.730213348
SNP_A-1997896 2.482192653
SNP_A-1997922 1.618513959
SNP_A-2000230 2.10632094
SNP_A-2000332 1.40315885
SNP_A-2000337 2.535997922
SNP_A-2000342 1.570974696
SNP_A-4268173 1.700030086

Total number of rows: 905422

Table truncated, full table size 22869 Kbytes.




Supplementary file Size Download File type/resource
GSM2522880_36315.CEL.gz 28.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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