|
| Status |
Public on Aug 16, 2012 |
| Title |
TAL1_shRNA1_Jurkat, biological replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Jurkat cells transduced with TAL1 shRNA1 for 72 hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat E6-1
|
| Treatment protocol |
The Jurkat cells were infected with shRNA lentivirus in the presence of polybrene by centrifugation at 2,500 rpm for 1.5 h followed by a incubation for overnight in a CO2 incubator. Total RNA was harvested after 3 days of infection.
|
| Growth protocol |
The Jurkat T-ALL cell line was grown in RPMI-1640 medium supplemented with 10% FBS, L-glutamine and penicillin/streptomycin at 37C in a CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen) followed by a column purification using RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from Jurkat cells transduced with TAL1 shRNA1 for 72 hrs
|
| Data processing |
Individual Arrays were normalized using Robust Multichip Averaging (RMA) within the Affytmetrix package from Bioconductor. Probeset definitions for RefSeq genes were derived from CDF version 13.0.0 downloaded from (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) based on improved definitions (Sandberg and Larsson, 2007).
|
| |
|
| Submission date |
May 10, 2011 |
| Last update date |
Aug 16, 2012 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13232 |
| Series (2) |
| GSE29179 |
Identification of differentially expressed genes upon shRNA knockdown of TAL1 and its regulatory partners in T-ALL cells (Jurkat) |
| GSE29181 |
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia |
|
