The chromatin accessibility and transcriptome comparison between nascent and fetal HSPCs. (A) Schematic representation of nascent HSPCs at 36 hours postfertilization (hpf) in the AGM region and fetal HSPCs at 3 days postfertilization (dpf) in the CHT region and the experimental flow to profile accessible chromatin and transcriptome in nascent and fetal HSPCs by ATAC-seq and RNA-seq. (B) GO analysis for genes with both accessible (left), decreased accessible in fetal HSPC (ie, nascent HSPC-specific accessible) (top right), and increased accessible in fetal HSPC (ie, fetal HSPC-specific accessible) (bottom right) chromatin regions. Enrichment scores were calculated by g:Profiler, and the enrichment network was performed by EnrichmentMap in Cytoscape. (C) Venn plot showing the overlap of genes with specific accessible chromatin regions and upregulated expression in nascent or fetal HSPCs, respectively. Genes for ATAC-seq were assigned by all ATAC-seq peak (see supplemental Gene Ontology (GO) analysis section). The P value shows the correlation significance between ATAC-seq and RNA-seq data at these 2 stages. P values were calculated by a 2-tailed χ² test. (D) Bar plot showing the percentage of “upregulated transcripts,” “no change transcripts,” and “downregulated transcripts” for genes with different states of accessible chromatin at nascent and fetal stages at promoters (left) and distal regulatory regions (right). (E) The genome browser views showing ATAC-seq and RNA-seq signals of genes specifically expressed in nascent HSPCs (left) or both in nascent and fetal HSPCs (right). FACS, fluorescence-activated cell sorter; FDR, false discovery rate.