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Sample GSM343962 Query DataSets for GSM343962
Status Public on Dec 01, 2008
Title YF004_NS_7; Montreal Cohort
Sample type RNA
 
Source name Whole Blood, Non stimulated, Day7
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) angerb@gmx.de
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.

Data table header descriptions
ID_REF ID corresponding to the probeID as found in manufacturer annotation file (Probe_ID).
VALUE Normalized log2 intensity
AVERAGE_SIGNAL Average bead intensity (raw data)

Data table
ID_REF VALUE AVERAGE_SIGNAL
ILMN_1804663 7 130.1104
ILMN_1651799 8.85 448.7941
ILMN_1782558 7 95.29424
ILMN_1812262 7.22 173.3382
ILMN_1712803 7 94.63748
ILMN_1774757 7 118.9673
ILMN_1712730 7 131.2694
ILMN_1813561 7 96.67863
ILMN_1761511 7 102.629
ILMN_1815941 7.13 165.3469
ILMN_1711451 7 102.0084
ILMN_1728255 7 109.6047
ILMN_1723582 7 126.0191
ILMN_1685843 7 101.7631
ILMN_1796374 7 121.0854
ILMN_1713272 7 86.04047
ILMN_1674380 7 103.998
ILMN_1660582 7.25 175.9526
ILMN_1717492 7 107.1344
ILMN_1811370 7 89.52781

Total number of rows: 22177

Table truncated, full table size 540 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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