|
| Status |
Public on Sep 01, 2011 |
| Title |
CD4+_Tcells_healthy_donor_1 |
| Sample type |
RNA |
| |
|
| Source name |
CD4_Tcells_healthy_donor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
batch: 1
age (years): 39
patient id: Control_1
fev1 (% predicted): 78
fvc (% predicted): 76
medication: None
cell type: CD4+ T-cells
|
| Treatment protocol |
Human CD4+ and CD8+ T cell were isolated by negative selection using Miltenyi beads and MACS Vario magnetic cell separation apparatus. T-cell purity was assessed by FACS using anti-CD4-FITC and anti-CD8-PE (Miltenyi) using CellQuest software.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion Europe) eluted in 50 ul RNase-free water (Promega UK) and purity was measured using a BioTek PowerWave XS (SSi Robotics, U.S.A.) spectrophotometer and Agilent Bioanalyser, which showed RIN values > 9.5.
|
| Label |
biotin
|
| Label protocol |
According to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridized to arrays at 45°C for 16 hr.
|
| Scan protocol |
Arrays were scanned with an Affymetrix scanner.
|
| Description |
Gene expression data from circulating T cells of healthy donor
|
| Data processing |
All steps of data preprocessing including background correction, normalization and expression set summaries were performed using the RMA algorithm in R/Bioconductor rma package. Batch effects corrected using the ComBat R package. Data was filtered to remove probes which had low expression in all arrays (rma signal value of < 4 was removed). Differential gene regulation was determined by taking the output from a shrinkage t-test ('st' R package), and then computing the p-values and q-values (FDR) using 'fdrtool' R package.
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Sep 01, 2011 |
| Contact name |
Ketan Anilkumar Patel |
| Organization name |
Pfizer
|
| Department |
WWRD
|
| Lab |
Computational Sciences CoE
|
| Street address |
Ramsgate Road
|
| City |
Sandwich |
| ZIP/Postal code |
CT13 9NJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE31773 |
Comparison of mRNA expression in circulating T-cells from patients with severe asthma |
|
