||We recruited 100 healthy, male donors of self-reported European descent (EUB) and 100 of self-reported African descent (AFB) (Ghent, Belgium). For each participant, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on Ficoll-Paque density gradients. Monocytes were then positively selected with magnetic CD14 microbeads and exposed for 6 hours to different ligands activating TLR4 (LPS), TLR1/2 (Pam3CSK4), TLR7/8 (R848) and to a human seasonal influenza A virus (IAV). High-quality RNA was obtained from unstimulated and stimulated monocytes for 970 of the 1000 samples (200 x 5 conditions), and was sequenced on an Illumina HiSeq2000. On average, 34 million 101-bp single-end reads were obtained per sample.
||Illumina HiSeq 2000
||Exome sequencing of 317 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. The population sample includes the Baka of south-eastern Cameroon and northern Gabon (wRHG), the Bantu-speaking Nzebi and Bapunu sedentary agriculturalists of Gabon (wAGR), and the BaTwa (eRHG) and BaKiga (eAGR) from Uganda. After QC filters, exomes of 300 unrelated individuals were obtained at high coverage (mean depth 68x), including 406,270 variants.
||Illumina HiSeq 2500
||Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists
||Illumina HumanOmni1-Quad-Illumina GenomeStudio
||Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanOmniExpress
||Genome-wide DNA methylation epigenotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanMethylation450
||The 100 European-descent (EUB) and 100 African-descent (AFB) Belgians studied were genotyped for a total of 4,301,332 SNPs on the Illumina HumanOmni5-Quad BeadChips. Whole-exome sequencing was carried out for the same 200 individuals with the Nextera Rapid Capture Expanded Exome kit, on the Illumina HiSeq 2000 platform, with 100-bp paired-end reads. This kit delivers 62 Mb of genomic content per individual, including exons, untranslated regions (UTR), and microRNAs. Omni5 and exome datasets were merged, yielding a concordance rate between platforms of 99.93%.
||Illumina HumanOmni5-Quad and exome sequencing
||Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study
||Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study
||Genome-wide SNP genotyping data for 102 Pakistani individuals by Illumina HumanOmni2.5-8 array, used in the EGAS00001002558 study
||Genotype data for 5,699,237 genotyped and imputed SNPs in the 816 healthy donors of the Milieu IntÃ©rieur cohort