|
| Status |
Public on Dec 01, 2008 |
| Title |
YF004_NS_3; Montreal Cohort |
| Sample type |
RNA |
| |
|
| Source name |
Whole Blood, Non stimulated, Day3
|
| Organism |
Homo sapiens |
| Characteristics |
Vaccinated Volunteer : YF004; Gender: F; Age: 21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNA extraction kits from Qiagen. Quantification was performed using NanoDrop Technologies spectrophotometer and RNA quality was assessed using the Experion automated electrophoresis system from Bio-Rad.
|
| Label |
biotin
|
| Label protocol |
Total RNA as amplified and labeled using the Illumina TotalPrep RNA Amplication kit which is based on the Eberwine amplification protocol. It involves a first cDNA synthesis step followed by in vitro transcription of cRNA.
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was hybridized onto Illumina Human RefSeq-8 BeadChips v2 at 58oC for 20 hours.
|
| Scan protocol |
Fluorescent array images were collected with Illumina BeadStation 500GX scanner fluorescent scanner and image intensity data were extracted using Illumina BeadStudio version 3 software.
|
| Description |
The Montreal Cohort enrolled 15 donors, and sampled whole blood pre vaccination with the Sanofi-Pasteur YF17D-204 YF-VAX vaccine, and on days 3,7,10,14,28,60,365 post vaccination.
|
| Data processing |
Illuma probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed. The R software was used to quantile normalize the probe intensities, and to minimum-replace (surrogate-replacement policy) values below background using the mean background vale of the probe controls rounded up to the rearest power of 2, determined from the microarray quality controls to reduce noise and reduce "over-inflated" expression ratios in subsequent steps.
|
| |
|
| Submission date |
Nov 19, 2008 |
| Last update date |
Nov 27, 2008 |
| Contact name |
Bastian Robert Angermann |
| E-mail(s) |
[email protected]
|
| Fax |
5143437854
|
| Organization name |
Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR-CHUM) Saint-Luc
|
| Lab |
Laboratoire d'immunologie
|
| Street address |
264 René-Lévesque Est
|
| City |
Montréal |
| State/province |
Quebec |
| ZIP/Postal code |
H2X 1P1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE13699 |
Immune response to the yellow fever vaccine 17D. |
|
