|
| Status |
Public on Aug 05, 2013 |
| Title |
peripheral blood T-cells of with newly diagnosed ITP 2 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood T-cells of with newly diagnosed ITP
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: newly diagnosed ITP
tissue: peripheral blood
cell type: T-cell
|
| Treatment protocol |
Cells were snap frozen in -80 C. Heparin anti-coagulated blood was obtained from each study subject. T-cells were isolated, in brief, peripheral blood mononuclear cells (PBMCs) were separated from the blood immediately after collection, by density gradient centrifugation. After removal of CD14+ cells by magnetic microbeads, T-cells were positively selected using CD3+ magnetic microbeads, according to the manufacturer's recommendations (MACS, Miltenyi Biotec, Surrey, UK).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))
|
| Label |
Biotin
|
| Label protocol |
Twenty ng of purified RNA was reverse transcribed, amplified and labeled using the Ovation amplification system V2 (NuGEN Technologies Inc, San Carlos, CA) according to the manufacturer's instructions. Five μg of the generated cDNA was fragmented and biotinylated using the Encore biotin module (NuGEN).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
After hybridisation (according to the Minimum Information About a Microarray Experiment guideline), the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).
|
| Description |
gene expression data from T-cell
|
| Data processing |
The raw expression signals were preprocessed following the method ofMASS5 (Affymetrix).The robust quantile method was applied to get normalized expression values
|
| |
|
| Submission date |
May 14, 2013 |
| Last update date |
Aug 05, 2013 |
| Contact name |
Intawat Nookaew |
| E-mail(s) |
inookaew@uams.edu
|
| Organization name |
University of Arkansas for Medical Sciences
|
| Department |
Department of Biomedical Informatics
|
| Street address |
4301 W Markham St
|
| City |
Little Rock |
| ZIP/Postal code |
72205 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE46922 |
Differences in gene expression and cytokines levels between newly diagnosed and chronic pediatric immune thrombocytopenia (ITP) |
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