|
| Status |
Public on Mar 03, 2016 |
| Title |
T013 |
| Sample type |
genomic |
| |
|
| Source name |
Type II Enteropathy-associated T-cell lymphoma Sample T013
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Tumor tissue
disease state: Type II Enteropathy-associated T-cell lymphoma
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from snap frozen patient specimens and whole blood was extracted using Blood & Cell Culture DNA Kit (Qiagen)
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to SNP6 array
raw B-allele frequency value; 'LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B (for the matche normal tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT)
|
| Data processing |
The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched normal CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.
|
| |
|
| Submission date |
Jul 08, 2015 |
| Last update date |
Mar 03, 2016 |
| Contact name |
Sanjanaa Nagarajan |
| E-mail(s) |
sanjanaa@duke-nus.edu.sg
|
| Organization name |
National Cancer Centre Singapore
|
| Department |
Department of Medical Sciences
|
| Lab |
NCCS-VARI Translational Research Laboratory
|
| Street address |
11 Hospital Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
169610 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE70653 |
Affymetrix Genome-Wide Human SNP Array 6.0 data for Type II Enteropathy-associated T-cell lymphoma |
| GSE70654 |
Type II Enteropathy-associated T-cell lymphoma |
|
