Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans [ATAC-seq]

Human subjects were vaccinated with seasonal influenza vaccine at day 0 (TIV, 2014-2015). A subgroup of subjects (abx) received an additional oral antibiotic regimen, consisting of neomycin, vancomycin, and metronidazole, between days -3 and 1. CD14+ monocytes, mDCs, and pDCs were isolated from PBMCs of vaccinated subjects (3 antibiotic treated, 5 controls) at day -21 (BL), 0 and 30 using FACS. ATAC-seq was used to analyze the chromatin accessibility landscape in these cells. Overall design: A total of 51 samples from 8 healthy donors (5x control, 3x antibiotics-treated) was analyzed. For each subject, three cell types were analyzed: CD14+ monocytes, mDCs, and pDCs. All subjects: d0 before vaccination and d30 after vaccination. PBMCs from antibiotics-treated subjects were additionally analyzed at d-21 before antibiotics treatment.