Fig 6

Expression profiling by RNA-seq of wild-type vs miR-34a-/- embryos at 8 and 72 hpf.

(A) Multi-dimensional scaling (MDS) 2-dimensional projection of RNA-seq count matrices for all samples. (B) Heatmaps of variance-stabilized transformed normalized counts (VST values) for samples at both stages with the numbers of genes up-regulated (UP) and down-regulated (DOWN) in miR-34a-/-. (C) KEGG pathway analysis for DEGs identified in the 8 hpf dataset. (D) KEGG pathway analysis for DEGs identified in the 72 hpf dataset. DEGs in 8 hpf and 72 hpf datasets were defined with fold-change ≥ 2 and FDR ≤ 0.05 as cut-offs. (E) REVIGO plot of Gene Ontology Biological Process terms identified for up-regulated genes in the 72 hpf dataset. (F) REVIGO plot of Gene Ontology Biological Process terms identified for down-regulated genes in the 72 hpf dataset. (G) Anatomical term enrichment using Zebrafish Expression Ontology of Gene Sets (ZEOGS) of both UP and DOWN-regulated genes in the 72 hpf dataset. Orange color indicates FDR q-value < 0.1 significance after Benjamini-Hochberg correction and green indicates P-value < 0.1 before correction.