|
| Status |
Public on Mar 01, 2011 |
| Title |
healthy control_3 |
| Sample type |
RNA |
| |
|
| Source name |
health control_3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
disease state: healthy control
|
| Treatment protocol |
Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation with Ficoll-Hypaque from freshly heparinized blood. The cells were washed in PBS and re-suspended at 1´106 cells/ml in complete medium RPMI-1640 for 48h before harvested for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from PBMC by RNeasy mini kit and treated with RNase-free DNase set, following manufacturer’s recommendation.
|
| Label |
biotin
|
| Label protocol |
A total of 100ng of total RNA was reverse transcribed to cDNA which was then used as template in an in-vitro transcription reaction followed by fragmentation of the single stranded cDNA and labeling through a terminal deoxy-transferase reaction. The biotinylated cDNA (5 µg) was fragmented
|
| |
|
| Hybridization protocol |
The biotinylated cDNA (5 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Gene 1.0 ST Array
|
| Scan protocol |
GeneChips were then scanned using GeneChip Scanner 3000 7G Plus 2 and Command Console Software (AGCC) version 1.0
|
| Data processing |
Raw gene expression data in the generated CEL files were then normalized using the GC Robust MultiChip Averaging (GC-RMA) algorithm as implemented in Bioconductor. To identify groups of functionally related genes that were differentially expressed, we conducted gene set analysis using the mixed effects models approach.
|
| |
|
| Submission date |
Aug 26, 2010 |
| Last update date |
Mar 01, 2011 |
| Contact name |
Fanglin Zhang |
| Organization name |
Vanderbilt University
|
| Street address |
2201 Childrens' way
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37212 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE23832 |
Expression profiles of PBMC from multiple sclerosis patients |
|
