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Sample GSM344070 Query DataSets for GSM344070
Status Public on Dec 01, 2008
Title Day14_YF1173; VaxDesign Mimic experiment
Sample type RNA
 
Source name Frozen stocks of autologous PBMCs were used as a source of lymphocytes.
Organism Homo sapiens
Characteristics Yellow Fever unexposed volunteer
Biomaterial provider Donald R. Drake,VaxDesign Corporation, 12612 Challenger Parkway, Suite 365, Orlando, FL 32826, USA
Treatment protocol Purified CD4+ T cells were co-cultured in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for 14 days
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 PBMCs used in the assays were acquired from normal healthy donors enrolled in a VaxDesign Corporation apheresis study program (protocol CRRI 0906009). Blood collections were performed at Florida’s Blood Centers (Olrando, FL) using standard techniques. The enriched leukocytes were isolated and cryopreserved. Human DCs were prepared as described in Gaucher et al. “Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses , J. Exp. Med XXX. After 5 days of culture with IL-4 and GM-CSF, the DCs were infected with a 1:100 dilution of the live-attenuated YF-VAX® vaccine. After 24 hrs, 5% human AB serum was added to the media to quench the infection. Alternatively, some of the DCs we not infected. On the sixth day, all DCs were matured with an overnight treatment of 25 ng/mL TNF- (R&D Systems).
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 GPL6883
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 38.58654
ILMN_1660305 7 69.02711
ILMN_1762337 7 31.34099
ILMN_2055271 7 41.30522
ILMN_1814316 7 29.79515
ILMN_2359168 7 28.6719
ILMN_1731507 7 27.4328
ILMN_1787689 7 31.86254
ILMN_1745607 7 34.35893
ILMN_2136495 7 29.56557
ILMN_1668111 7 27.19695
ILMN_2295559 7 33.53637
ILMN_1735045 7 36.39339
ILMN_1680754 7 25.79035
ILMN_2375184 7 30.45491
ILMN_1659452 7 37.1069
ILMN_1767388 7 32.94529
ILMN_1675204 7 31.02505
ILMN_1673870 7 30.3022
ILMN_1755321 7 46.51323

Total number of rows: 24526

Table truncated, full table size 584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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