Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

Inflammatory responses occur within the complex spatial context of tissues and organs, and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here, we used single-cell RNA sequencing to screen for genes differentially expressed under LPS (lipopolysaccharide) and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS (P. Aeuruginosa, Sigma), or E3 alone (vehicle control), for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium 3' platform and reagents (v3.1 kit) was used for cell encapsulation, reverse transcription, and library preparation, according to manufacturer instructions (manual revision D), with 12 cycles of preamplification.