|
| Status |
Public on Nov 27, 2021 |
| Title |
extranodal NKTL,NKTL16A,FFPE Preparation |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE
disease: extranodal NKTL
type: AT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA from FFPE tissue samples were extracted by using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Invitrogen™.
|
| Label |
biotin
|
| Label protocol |
Each of the DNA samples were annealed with MIP (Molecular Inversion Probe) linear probe according to the Affymetrix OncoScanCNV protocol.
|
| |
|
| Channel 2 |
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE
disease: extranodal NKTL
type: GC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA from FFPE tissue samples were extracted by using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Invitrogen™.
|
| Label |
biotin
|
| Label protocol |
Each of the DNA samples were annealed with MIP (Molecular Inversion Probe) linear probe according to the Affymetrix OncoScanCNV protocol.
|
| |
|
| |
| Hybridization protocol |
MIP probe annealing and hybridization to Affymetrix OncoScanCNV Arrays was performed according to manufacturer's protocols.
|
| Scan protocol |
Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols.
Arrays were scanned using the Affymetrix 3000 7G scanner according to manufacturer's protocols.
|
| Description |
Genomic copy number data from Homo sapiens extranodal NKTL samples by Affymetrix OncoScan FFPE Assay
sample name:
NKTL16A
|
| Data processing |
Data is processed using Affymetrix OncoScan Console (v1.3) software.
Processed data files includes: Median Log2 Ratio
Median Log2 Ratio: log2 ratio of the normalized intensity of the sample over the normalized intensity of a reference with further correction for sample specific variation.
The reference for calculating log2 normalized intensity ratio is normal diploid markers identified in the cancer samples. This normal diploid region is the region without any copy number gain and loss in the cancer samples, and it can be identified automatically or manually in the software (oncoscan console,v1.3).
|
| |
|
| Submission date |
Oct 26, 2020 |
| Last update date |
Nov 27, 2021 |
| Contact name |
Siok-Bian Ng |
| E-mail(s) |
patnsb@nus.edu.sg
|
| Organization name |
National University Health System, Singapore
|
| Department |
Department of Pathology
|
| Street address |
National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3
|
| City |
Singapore |
| ZIP/Postal code |
119074 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18602 |
| Series (2) |
| GSE160118 |
Minimal Genomic Instability and Increased Immune Activity Differentiate EBV-positive PTCL from ENKTL and PTCL NOS [CNA] |
| GSE160120 |
Minimal Genomic Instability and Increased Immune Activity Differentiate EBV-positive PTCL from ENKTL and PTCL NOS |
|
