|
| Status |
Public on Sep 14, 2018 |
| Title |
AITL_Patient_Sample_TAITL49 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor tissue from AITL patient
|
| Organism |
Homo sapiens |
| Characteristics |
tet2 status: Angioimmunoblastic T-Cell lymphoma (AITL)
diagnosis: Mutant
rhoa status: Mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol, 10ug of RNAeasy-purified total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G
|
| Description |
Gene expression profiling of AITL tumors
|
| Data processing |
CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF was used to reannotate the probes (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/entrezg.asp). The samples were normalized in RMA together with some normal T cell samples from GEO (GSM146182-GSM146196).
|
| |
|
| Submission date |
Oct 22, 2013 |
| Last update date |
Sep 14, 2018 |
| Contact name |
Weng Khong Lim |
| E-mail(s) |
wengkhong.lim@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 |
GPL17811 |
| Series (1) |
| GSE51521 |
Gene expression profiling of Angioimmunoblastic T-Cell lymphoma (AITL) tumors |
|
