Whole-transcriptome RNA-seq analysis of zebrafish microglia subpopulations

We generate whole-transcriptome RNA-seq profiles of microglia subpopulations in the adult zebrafish brain (4-month-old) to study their heterogeneity. Cells were isolated as ccl34b.1+mpeg1+ populations or ccl34b.1-mpeg1+ populations from the whole brain of double transgenic TgBAC(ccl34b.1:eGFP);Tg(mpeg1:DsRedx) fish. ccl34b.1+mpeg1+ and ccl34b.1-mpeg1+ microglia were grouped into two distinct clusters in the Principal component analysis (PCA), and we identified substantial differentially-expressed genes between these two microglial populations using the DESeq2 package. To further unveil their differential roles during inflammation, we injected E. coli into the brain ventricles of adult zebrafish and isolated both populations for whole-transcriptome RNA-seq. This RNA-seq profile provides valuable information for dissecting their respective functions in vivo. WT experiment: 5 fish in total; each fish sorted 100 ccl34b.1+mpeg1+ cells and 100 ccl34b.1-mpeg1+ cells with 3 technical replicates; 1 technical replicate processed for RNA-seq based on the cDNA quality. E. coli injection experiment: 9 fish in total; 2 control fish, 4 pbs injected fish, 3 E. coli injected fish; each fish sorted 100 ccl34b.1+mpeg1+ cells and 100 ccl34b.1-mpeg1+ cells with 3 technical replicates; 1 technical replicate processed for RNA-seq based on the cDNA quality.