Fig. 1

Experimental design and cell clustering. Diagrammatic figure showing the experimental design and workflow. Briefly, four SHK-1 cell plates were seeded at the same time, and three plates were infected 24 h, 48 and 96 h prior to harvesting. The four plates were collected 120 h post seeding, and immediately processed using the 10x workflow for single-cell RNA-seq library preparation. Libraries were sequenced using Illumina technology, and processed using Alevin and Seurat (see Methods) to cluster the cells of each sample according to their transcriptome