|
| Status |
Public on Oct 22, 2012 |
| Title |
HCV_p04 [Affymetrix] |
| Sample type |
RNA |
| |
|
| Source name |
Human PBMC collected from whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell: PBMC
infection: HCV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was collected from a group of 10 patients who were infected with genotype 1 hepatitis C, before initiation of treatment at the Indiana University School of Medicine. Control blood samples were harvested from healthy student volunteers. Peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of the cohort using centrifugation through a 10-ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ), and RNA was isolated within a few hours.
|
| Label |
biotin
|
| Label protocol |
Preparation of cDNA, cRNA, and labeling were carried out according to the protocols recommended by Affymetrix in the GeneChip® Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
|
| Scan protocol |
The microarrays were scanned using a dedicated Model 3000 scanner controlled by GCOS software.
|
| Description |
Human PBMC collected from whole blood of patients chronically infected with HCV, before initiation of therapy
|
| Data processing |
Microarray data was normalized using the GCRMA package in bioconductor. After normalization, Principle Component Analysis (PCA) was used to identify major patterns in the data, which revealed that the HCV samples were split into two groups based on the sample preparation time. Batch correction techniques were applied to remove these effects, and the data then separated into two distinct groups representing the healthy and HCV samples.
|
| |
|
| Submission date |
Aug 17, 2012 |
| Last update date |
Oct 23, 2012 |
| Contact name |
Christopher Bolen |
| E-mail(s) |
[email protected]
|
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
Steven Kleinstein
|
| Street address |
300 George Street, Suite 505
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE40184 |
The blood transcriptional signature of chronic HCV [Affymetrix data] |
| GSE40224 |
The blood transcriptional signature of chronic HCV |
|
