Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [Ss2_pDC1]

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 (MCMV) infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain. This dataset corresponds to splenic pDCs sorted from Ifnb1Eyfp reporter mice that were untreated or had been infected for 36 hours 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 two 96-well plates. Plate 1 corresponded to pDCs from uninfected mice. Plate 2 corresponded to pDCs from infected animals, with enrichment of IFN-I+ pDCs by index sorting of 33 YFP+ cells. In each plate, two 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.