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Sample GSM343925 Query DataSets for GSM343925
Status Public on Dec 01, 2008
Title YF016_NS_10; Montreal Cohort
Sample type RNA
 
Source name Whole Blood, Non stimulated, Day10
Organism Homo sapiens
Characteristics Vaccinated Volunteer : YF016; Gender: M; Age: 23
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 7.02 81.07157
ILMN_1651799 8.88 270.5829
ILMN_1782558 7 43.82894
ILMN_1812262 7.33 96.44537
ILMN_1712803 7 54.43521
ILMN_1774757 7 59.3662
ILMN_1712730 7 74.85556
ILMN_1813561 7 50.09906
ILMN_1761511 7 52.48492
ILMN_1815941 7 71.90662
ILMN_1711451 7 49.83756
ILMN_1728255 7 57.39125
ILMN_1723582 7 65.05861
ILMN_1685843 7 52.79576
ILMN_1796374 7 59.81614
ILMN_1713272 7 39.63086
ILMN_1674380 7 53.92693
ILMN_1660582 7.59 113.119
ILMN_1717492 7 54.40039
ILMN_1811370 7 42.14479

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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