Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [FB5P-seq_kinetic]

The aim of the project is to characterize the heterogeneity of murine plasmacytoid dendritic cells (pDCs) and to decipher their activation trajectory during a viral infection in vivo. To this end, individual splenic pDCs were transcriptionally profiled at ground state and at different times during mouse cytomegalovirus infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain and on their downregulation of LIFR. Overall design: This dataset contains data from pDCs sorted from Ifnb1Eyfp reporter mice at different time points after murine cytomegalovirus (MCMV) infection. Single-cells were FACS-sorted into fifteen 96-well plates. One plate of total pDCs was sorted from one uninfected mouse. For the infected mice, pDCs were sorted into 4 different phenotypic populations, to have a view of the total pDC population (gate: pDC total) as well as to enrich the pDCs that were committed to, or fate-mapped for, IFN-I production (gates: pDC LIFRlo/neg, pDC LIFRlo/neg YFP+, pDC LIFR+ YFP+). Nine plates were sorted for the mouse infected for 33 hours, 3 plates for 36 hours and 2 plates for 48 hours. Gene expression was profiled by 5'-end single-cell RNAseq following the FB5P-seq protocol.