“…To identify cell types and states at chosen clustering resolution (0.6 for control only, 0.5 for control and infected integrated), we performed differential expression analysis using Wilcoxon rank sum-based method (log2 fold change > 0.25, % of expressing cells > 0.25). Known markers were used to identify T cells ( cd247l , lck , il7r , and cxcr4a ) ( 58 – 60 ), dendritic cell-like populations ( ctsbb , tlr7 ) ( 61 , 62 ), B cells ( cd37 , pax5 ) ( 63 , 64 ), macrophages ( mpeg1.1 , grn1 ) ( 65 , 66 ), neutrophils ( mpx , il6r ) ( 11 , 67 ), erythrocytes ( hbba2 , hemgn ) ( 68 ), thrombocytes ( thbs1b , fn1b ) ( 62 ), superficial epithelial cells ( krt1-19d , cldne ) ( 69 ), ionocytes ( trpv6 , foxi3b ) ( 70 ), intermediate epithelial cells ( cldna , tp63 ) ( 69 ), basal epithelial cells ( cldn1 , cldni ) ( 69 ), mesenchymal cells ( vcana , clu ) ( 71 ), lateral line-like cells ( prox1a , prr15la ) ( 72 ), and epidermal mucous cells ( agr2 , cldnh ) ( 69 ). We found one population with some cells locating closer to the T cell populations but without clear enrichment for known signatures and included this population for a subclustering analysis with other T cells.…”