NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM344043 Query DataSets for GSM344043
Status Public on Dec 01, 2008
Title YF18BL; Lausanne Cohort
Sample type RNA
 
Source name Whole Blood, Non stimulated, Day 0
Organism Homo sapiens
Characteristics Non Vaccinated Volunteer :YF18; Gender;F : Age:23
Biomaterial provider Giuseppe Pantaleo,Division of immunology and allergy, Department of medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
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 In the Lausanne Cohort 11 donors were enrolled vaccinated with Stamail, wohle blood was sampled on days 0,3 and 7.
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_1809034 7 121.6984
ILMN_1660305 7 154.797
ILMN_1792173 7.23 220.1582
ILMN_1762337 7 54.95434
ILMN_1736007 7 65.35958
ILMN_1787689 7 77.2299
ILMN_1731507 7 63.95545
ILMN_1814316 7 69.78204
ILMN_1745607 7 60.83992
ILMN_1757454 7 73.9197
ILMN_1735045 7 73.97159
ILMN_1680754 7 108.3373
ILMN_1659452 7 59.08691
ILMN_1767388 7 168.6463
ILMN_1673870 7 60.18515
ILMN_1675204 7 65.53603
ILMN_1755321 7 125.5541
ILMN_1698554 7 177.7271
ILMN_1805938 7 62.6375
ILMN_1676336 7 107.9681

Total number of rows: 22184

Table truncated, full table size 539 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap