|
| Status |
Public on Sep 24, 2015 |
| Title |
Patient 11, Tumor Sample, Location 3 |
| Sample type |
genomic |
| |
|
| Source name |
Patient 11, Tumor Sample, Location 3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 75
tumor stage: pT3N2M0
tumor size (cm): 7.5
tissue: rectum
number of nodes positive: 3
surgery: Total Proctocolectomy
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from frozen tissue, using the Allprep mini kit (Qiagen, Valencia, California) and according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan (P/N 703175 Rev. 1).
|
| |
|
| Hybridization protocol |
Arrays were hybridized overnight (17 hrs). Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody using parallel GeneChip Fluidics 450 stations.
|
| Scan protocol |
Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software
|
| Data processing |
CEL files are combined by Affymetrix OncoScan Console software to generate OSCHP files, which are analyzed by Nexus Copy Number by BioDiscovery using the TuScan algorithm (which is Affymetrix's version of the ASCAT algorithm)
Probe intensities. B-allele frequency, and Allelic imbalance measurements across 217K probe locations
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
Sep 24, 2015 |
| Contact name |
Ana Rodrigues Grant |
| E-mail(s) |
anapcr@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Computational Medicine & Bioinformatics
|
| Street address |
100 Washtenaw Avenue
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE73365 |
Intra-tumor Genetic Heterogeneity in Rectal Canger |
|
