|
| Status |
Public on Oct 22, 2012 |
| Title |
HCV_SK3 [Illumina] |
| Sample type |
RNA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell: PBMC
infection: HCV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Treatment-naïve HCV patients were recruited by hepatologists in the outpatient hepatitis clinic within the Yale Liver Center. Healthy volunteers were recruited from Yale’s PhenoGenetic Cohort of Healthy controls. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) centrifugation. Total RNA was isolated from PBMCs using an RNeasy kit (Qiagen, Valencia, CA), and the quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on an Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.
|
| |
|
| Hybridization protocol |
1.5 µg of cRNA was combined with hybridization controls and hybridized to the array for 16 hours in a hybridization oven at 58°C. The chip was then washed and stained with streptavidin-Cy3.
|
| Scan protocol |
The array was scanned using the Illumina BeadArray reader.
|
| Description |
Human PBMC collected from whole blood of patients chronically infected with HCV, before initiation of therapy
|
| Data processing |
Microarray data from the validation cohort underwent quantile normalization using the Beadarray package in bioconductor.
|
| |
|
| Submission date |
Aug 20, 2012 |
| Last update date |
Oct 22, 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 |
GPL10558 |
| Series (2) |
| GSE40223 |
The blood transcriptional signature of chronic HCV [Illumina data] |
| GSE40224 |
The blood transcriptional signature of chronic HCV |
|
