|
| Status |
Public on Jun 06, 2018 |
| Title |
Normal_6454 |
| Sample type |
RNA |
| |
|
| Source name |
Normal sample from prostate cancer patient 6454
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: prostate cancer patient
subject id: patient 6454
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 |
36055
|
| 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 |
|
