snRNAseq analysis of mouse placenta during ZIKV infection

The aim of this study was to study placental immune responses to ZIKV infection at the cell level. WT or MAVS-deficient placentas from mock- or ZIKV- infected pregnant WT or mutant mice were collected, and placentas from male fetuses selected to facilitate the identification of maternal and fetal clusters, and doublets. Two placentas from the same genotype and condition were pooled and processed for isolation of nuclei. Approximately 10,000 nuclei per sample were subjected to gel bead-in-emulsion (GEM) generation, reverse transcription, and construction of libraries for sequencing according to the protocol provided in the 3' gene expression v3.1 kit manual (10X Genomics). We obtained 98,661 nuclei with a median of 3,077 genes detected per nucleus after data processing and quality control. Seurat integrated analysis and graph-based clustering identified cell types in maternal and fetal compartments based on analysis of canonical cellular markers. We performed differential expression test using Wilcoxon test from Seurat to identify the changes in expression across conditions. The DSGs were then used to align to the Hallmark mouse pathway database Msigdbr (Version 7.5.1) with package fgsea (Version 1.26.0) and pathways that with P-adjusted value < 0.05 were chosen as the significantly enriched pathways. We found cell-type specific antiviral pathways driven by MAVS, and MAVS-independent induction of interferon-stimulated and antiviral genes in other cell types.