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Figure 1 Transcriptional profiling of infarcted hearts under regenerative and macrophage-delayed conditions. (A) Experimental design. Zebrafish AB_wildtype was IP-injected with PBS or clodronate liposomes (CL) 1 d before cardiac cryoinjury. Injured hearts were collected at 7 and 21 days post cryoinjury (dpci), respectively. Uninjured hearts were collected as the control of the baseline. Total RNA was extracted and analyzed by RNA sequencing (RNAseq). (B) Principal component analysis (PCA) of gene expression in hearts at different time points. The PCA was performed on the FPKM normalized datasets of healthy hearts and injured hearts at 7 and 21 dpci after PBS or CL treatments (PBS7d, PBS21d, CL7d, and CL21d). The datasets of 0 hr, 6 hr, 1d, 2d, 3d, and 5 dpci from the previous study were also included (Lai et al., 2017). Regeneration and delayed dynamics are indicated by purple and green lines, respectively. FPKM, Fragments Per Kilobase of transcript per Million mapped reads. (C) Hierarchical clustering heatmap of the comparatively DEGs under regenerative and macrophage-delayed conditions in zebrafish. The DEGs were selected by NOIseq (q > 0.99) and arranged by hierarchical clustering from cluster 1 (C1) to cluster 22 (C22) (left panel). The value was a z-score from 1.5 as red to –1.5 as blue. BP of GO and KEGG pathways of the DEGs were analyzed by using WebGestalt (right panel). Cluster-enriched genes involved in their predicted biological processes and pathways were listed. The threshold of enriched categories was FDR < 0.05. DEGs, differentially expressed genes; GO, Gene Ontology; BP, biological process; KEGG, Kyoto Encyclopedia of Genes and Genomes; FDR, false discovery rate.