|
| Status |
Public on Feb 09, 2017 |
| Title |
Leukocyte TP12-S0918 |
| Sample type |
genomic |
| |
|
| Source name |
Leukocyte TP12-S0918
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Leukocyte
patient: TP12-S0918
age: 60
Stage: T3bN1MX
gleason: 5+4=9
nomogram 5 years: 0.63
recurrence label: yes
fast relapase label: f
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Qiagen blood DNA extraction kit.
|
| Label |
Biotin
|
| Label protocol |
The fragmented DNA was labeled with biotinylated nucleotides through terminal deoxynucleotide transferase for 4 hours at 37oC, following the manual provided by Affymetrix, Inc.
|
| |
|
| Hybridization protocol |
Two hundred fifty micrograms of fragmented DNA were hybridized with a pre-equilibrated Affymetrix chip SNP 6.0 at 50oC for 18 hours. Procedures of washing and scanning of SNP 6.0 chips followed the manuals provided by Affymetrix, Inc.
|
| Scan protocol |
The hybridized chips were scanned by 7G Affymetrix scanner.
|
| Description |
Affymetrix SNP 6.0
|
| Data processing |
CEL files were analyzed with Genotyping Console for quality control analysis. Samples with QC call above 80% and QC contrast ratio above 0.4 were admitted into the analysis. To analyze CNV, CEL files were imported into Partek GenomeSuite 6.6 to generate copy number from raw intensity.
Each CEL file represents data from one patient. Deletion or amplification of genomes were analyzed by first limiting to the regions with p-value less than 0.001. The selected regions were subsequently filtered by limiting to the regions with at least 10 markers and 2 kb in size.
|
| |
|
| Submission date |
Jul 08, 2015 |
| Last update date |
Feb 09, 2017 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
silvia.shuchang.liu@gmail.com
|
| Organization name |
University of Pittsburgh
|
| Street address |
130 De Soto Street
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE70650 |
Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes |
|
