|
| Status |
Public on Nov 22, 2017 |
| Title |
CP08_T2 |
| Sample type |
genomic |
| |
|
| Source name |
Patient CP08, primary tumor sample, location 2
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 62
tumor stage: T3N1M0
tissue: Colon cancer tumor CP08, primary , location 2
location: Transverse colon
number of nodes positive: 2
tissue type: fresh frozen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from 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 v.1.1.0 software (ThermoFisher, Waltham, Massachusetts) to generate OSCHP files, which are analyzed by Nexus Copy Number v7.5 (Biodiscovry, El Segundo, California) using their SNP-FASST2 segmentation algorithm.
Probe intensity data at 50-100kb resolution across a set of 891 cancer genes and 300-400kb across the rest of the genome are generated, resulting in a median Log2 Ratio and a median B-allele frequency (BAF) measurement for each genomic segment.
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Karin Hardiman |
| E-mail(s) |
kmha@med.umich.edu
|
| Phone |
734-647-9710
|
| Organization name |
University of Michigan
|
| Department |
General Surgery
|
| Lab |
Hardiman Lab
|
| Street address |
2922F Taubman Center
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109-5300 |
| Country |
USA |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE107225 |
Lymph Node Metastases in Colon Cancer are Polyclonal |
|
