|
| Status |
Public on Feb 29, 2016 |
| Title |
ATRA treated activated CD4 cells, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: In vitro activated CD4 cells
|
| Treatment protocol |
Cells (10^6/ml) were treated with anti-CD3 antibodies immobilized (10 mg/ml in PBS) on polystyrene surfaces in presence or absence of 2 µM of all-trans-retinoic acid. After 48 h of incubation cells were harvested and total cellular RNA was isolated.
|
| Growth protocol |
Human Peripheral blood mononuclear cells (PBMCs) were purified by Histopaque density gradient centrifugation from lymphapheresis of healthy donors. CD4 lymphocytes were isolated using Dynal beads and were maintained in RPMI medium supplemented with 10 mM HEPES buffer, 2 mM L-glutamine, 60 mg/ml gentamicin, rIL-2 (20 units/ml), and 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneast mini kit
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
In vitro activated CD4 cells
|
| Data processing |
Data was processed using Partek Pro. RMA normalization and mean gene summary was performed
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Oct 22, 2015 |
| Last update date |
Feb 29, 2016 |
| Contact name |
Ven Natarajan |
| Organization name |
Leidos Biomedical Research Inc
|
| Street address |
Bldg 550/121
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE74280 |
Effect of retinoic acid on gene expression in CD4 cells stimulated with anti CD3 and CD28 |
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