Table 1.

Detailed comparison between three yellow fever vaccine studies.

#	Comparison item	Gaucher et al., 2008	Scherer et al., 2007	Querec et al., 2009
1	Location of study	Montreal, Canada Lausanne, Switzerland Emory University, US	University of Washington, US	Emory Vaccine Center, US
2	Human subjects	Montreal cohort, 20 volunteers Lausanne cohort, 13 volunteers Emory cohort, 10 volunteers	20 healthy humans aged 18–40	15 healthy humans aged 18–45
3	Vaccine*	Sanofi-Pasteur YF-VAX	Sanofi-Pasteur YF-VAX	YF-17D
4	Vaccination frequency	Single	Single	Single
5	Vaccination dose	0.5 mL per dose	N/A	N/A
6	Vaccination route	Subcutaneous injection	N/A	N/A
7	Specimen	Blood samples	Blood samples	Blood samples
8	Sample preparation	50 mL blood drawn, anti-coagulation using heparin, PBMCs prepared	20 mL blood drawn, anti-coagulation using citrate, PBMCs prepared, resuspended in RNAlater, stored frozen at −20°C	Blood drawn, anti-coagulation using citrate, PBMCs prepared, lyzed with TRIzol (Invitrogen), stored at −80°C
9	Sample preparation data	Day 0, 3, 7, 10, 14, 28, 60 after vaccination	Day 0, 4–8 days after vaccination	Day 0, 1, 3, 7 and 21 after vaccination
10	RNA preparation	Qiagen PaxGene	RNeasy Mini Kits (Qiagen)	TRIzol (Invitrogen)
11	RNA amplification	Illumina RNA Amplification Kit	Low RNA Input Fluorescent Linear Amplification Kit	Two-round amplification using Affymetrix protocol
12	Process afterwards	cDNA synthesis → cRNA synthesis	Cy3/Cy5 two-color labeling, hybrization	Affymetrix GeneChip protocol
13	Microarry chip type	Illumina Human RefSeq-8 BeadChips v2	Agilent human 1 cDNA microarrays, and Human 1A Oligo Microarray Kit (V2)	Affymetrix Human Genome U133 Plus 2.0 Array
14	Microarry scanner	Illumina BeadStation 500GX scanner	Perkin Elmer ScanArray Express dual-laser microarray scanner	GeneChip Scanner 3000 (Affymetrix)
15	Raw data process software	Illumina BeadStudio v3 software	N/A	Affymetrix GCOS software
16	Gene expression filtering	Filter out probes with intensities below background	N/A	Filtering based on a threshold of normalized fold change
17	Gene expression data analysis method	BioConductor LIMMA	R LIMMA package A moderated empirical Bayes t-statistic and p-value	R package
18	Gene annations	Unclear	UniGene build 133	UniGene build 133
19	# genes identified	594	615	97
20	Gene enrichment	GO enrichement for TF analysis	GO enrichement	Not done

^*All three studies use YF-17D vaccine. YF-VAX is a brand name of the YF-17D vaccine manufactured at Sanofi-Pasteur.