Fig 2

elf3 genotype and microbial status have significant effects on the larval zebrafish transcriptome. (A) Schematic depicting the experimental conditions of the bulk RNA-seq experiment where clutches of elf3^+/+ and elf3^−/− larvae produced from homozygous incrosses were derived GF. At 3 days post-fertilization (dpf), half of the larvae from each genotype were colonized with a conventional zebrafish microbiota (CV) (indicated with solid or dashed lines), and all groups were maintained until a 6 dpf endpoint, at which point pooled larval samples were prepared for sequencing (n = 6–16 larvae per pool). (B) principal component analysis (PCA) plot of the normalized counts for each replicate of the four experimental conditions (GFWT:3, GFMut:4, CVWT:4, CVMut:5). (C) Venn diagram overlap of the genes significantly differentially expressed (P adjusted < 0.05) in the four comparisons. (D) Metascape (61) analysis of the enriched GO terms, biological processes, and signaling pathways that are upregulated (red lettering) and downregulated (blue lettering) in each of the four RNA-seq comparisons. Abbreviations: NSCM metabolic process, nucleobase-containing small molecule metabolic process; modified amino acid MP, modified amino acid metabolic process; metabolism of AAs & derivatives, metabolism of amino acids and derivatives. (E) Scatterplot of the gene log₂ fold change for all significant differentially expressed genes in the CVWT/GFWT and CVMut/GFMut RNA-seq comparisons (P adjusted < 0.05), which assess the effect of microbial status on gene expression. (F) Scatterplot of the gene log₂ fold change for all significant differentially expressed genes in the GFMut/GFWT and CVMut/CVWT RNA-seq comparisons (P adjusted < 0.05), which assess the effect of elf3 genotype on gene expression.