Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [Ss2_pDC2]

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 the time of their peak production of type I interferon (IFN-I) during mouse cytomegalovirus infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain and on their down-regulation of LIFR. This dataset contains data from pDCs sorted from Ifnb1Eyfp reporter mice infected or not with murine cytomegalovirus (MCMV). pDCs were gated as Viable cells [live/dead cell dye (neg/low)], Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), singlet, CD11c(low/int), CD317(pos/high) cells. Single-cells were FACS-sorted into four 96-well plates. Plate 1 corresponded to pDCs from one uninfected mouse, sorted into two different populations: LIFRlow and LIFRhigh. Plate 2 to 4 corresponded to pDCs from one infected mouse, sorted into five different phenotypic populations: LIFRhigh, LIFRlowBST2high, LIFRhighYFPpos, LIFRlowYFPpos and LIFRlowBST2low; YFP was negative unless mentioned otherwise. In each plate, 2 or 3 wells were included as bulk population controls. Gene expression was analyzed by single-cell RNAseq following the Smart-Seq2 protocol. The data from control wells are not included here.