|
| Status |
Public on Oct 01, 2013 |
| Title |
PMA treated, doxycycline treated; biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
U937-derived cell line harboring TRIPZ-shRNAmir TetOn cassette (clone ID: V3THS-381738)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
cell type: histiocytic lymphoma
genotype/variation: ZXDC1 knockdown
agent: PMA
|
| Treatment protocol |
Individual cell lines were treated with 0.5 ug/mL doxycycline every day for four days to achieve inducible knockdown of ZXDC1/2. After the first two days of doxycycline treatment, cell lines were treated with either 100 nM PMA or vehicle (0.1% DMSO) and allowed to differentiate for 3 days.
|
| Growth protocol |
U937 stably transduced with TRIPZ-shRNAmir (Thermo/OpenBiosystems) were cultured in RPMI + 10% FBS, 100 U/mL penicilli, 100 ug/mL streptomycin, and 0.5 ug/mL Puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted via Qiagen Rneasy Micro kit according to the manufacturer's instruction
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the GeneChip 3' IVT Express kit from 100 ng total RNA (Affymetrix catolog # 901228).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in a GeneChip hybridization oven 640. GeneChips were singly scanned using a Genechip scanner 3000 7G with autoloader. Fluidics and scan functions were controlled by Command Console software ver 1.1 (AGCC).
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Dox_PMA_3
Gene expression data from cell line differentiated with PMA in the presence of doxycycline-inducible knockdown of ZXDC1/2
|
| Data processing |
The data were analyzed with AltAnalyze version 2.02 beta, using RMA for normalization.
|
| |
|
| Submission date |
Mar 22, 2013 |
| Last update date |
Oct 01, 2013 |
| Contact name |
Joseph Fontes |
| E-mail(s) |
jfontes@kumc.edu
|
| Organization name |
Univ Kansas Medical Center
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
3901 Rainbow Blvd
|
| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE45417 |
Expression data from knockdown of ZXDC1/2 in PMA-treated U937 |
|
