|
| Status |
Public on Feb 08, 2010 |
| Title |
Angioimmunoblastic T-cell lymphoma 3 |
| Sample type |
RNA |
| |
|
| Source name |
Pre-treated fresh frozen biopsy, PTCL
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PTCL
age: 77
gender: male
|
| Treatment protocol |
The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.
|
| Growth protocol |
All the tissues used in the study were fresh frozen and stored below -70 degree C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Affymetrix Scanning Protocol.
|
| Description |
Gene expression data from PTCL pre-treated biopsy.
CLN-138
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).
|
| |
|
| Submission date |
Nov 17, 2009 |
| Last update date |
Feb 21, 2023 |
| Contact name |
Javeed Iqbal |
| E-mail(s) |
jiqbal@unmc.edu
|
| Phone |
402-559-7753
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pathology and Microbiology
|
| Lab |
Center for Research in Leukemia and Lymphoma
|
| Street address |
40th street
|
| City |
omaha |
| State/province |
NE |
| ZIP/Postal code |
68195 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE19069 |
Molecular signatures in peripheral T-cell lymphoma (PTCL) |
|
| Relations |
| Reanalyzed by |
GSE65823 |
| Reanalyzed by |
GSE119087 |
| Affiliated with |
GSM7055564 |
