Fig. 5.

Loss of Prdm1a leads to downregulation of important limb development genes in the pectoral fin. RNA-seq was performed on isolated pectoral fin cells from about 250 WT and prdm1a^−/− embryos at 48 hpf. (A) Lateral and (A′) dorsal view of EGFP-positive pectoral fins from the Tg(Mmu:Prx1-EGFP) zebrafish line at 48 hpf before FACS. Dashed lines indicate where the embryos were dissected prior to FACS. Scale bars: 200 µm. (B) Heat map of top 250 differentially expressed genes (P_adj) between WT and prdm1a^−/− embryos. (C) Volcano plot showing spread of differentially expressed genes in pectoral fins of prdm1a^−/− compared to WT embryos. Light blue dots are significant, differentially expressed genes [−log₁₀(P-value)≥1.15]. Purple dots are downregulated, selected genes of interest, whereas yellow dots are upregulated genes. (D) Downregulated genes in prdm1a^−/− embryos were subjected to GO (Panther) pathway enrichment analysis. Yellow arrowheads highlight pathways of interest. A, anterior; ba, branchial arches; DEG, differentially expressed genes; e, eye; P, posterior; pf, pectoral fin; y, yolk.