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. 2017 Oct 16;125(10):107006. doi: 10.1289/EHP1937

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Figure 1A is a bubble plot. Figure 1B is a scatter plot with a reference line for which x=y, to represent a fold change of zero. Figure 1C is a heat map of differentially accessible regions of CAST/EiJ and C57BL/6J mice, along with a dendogram. The mean-centered normalized chromatin accessibility ranges from negative 3 to 3. Figure 1D shows sequence reads of representative loci Exo1, and Rbck1 and Trib3 in CAST/EiJ and C57BL/6J mice. — Strain-specific transcriptome dynamics, microRNA (miRNA) profiles, and chromatin accessibility in the mouse lung without exposure to 1,3-butadiene. (A) Bubble plot showing enriched reactome pathways for differentially expressed genes more highly expressed in CAST/EiJ control mice compared with those more highly expressed in C57BL/6J control mice. For each pathway, significance is represented by shading, and the number of genes in each pathway is represented by bubble size. For clarity, groups of related pathways are labeled with a general descriptive term as opposed to individual pathway names. A false discovery rate $(FDR) of < 10 %$ was used to determine significance, but owing to the number of significant pathways, only the top 105 pathways in either direction are shown (see Excel Table S3 for a complete list). (B) Average expression of miRNAs in CAST/EiJ control (x-axis) compared with C57BL/6J control (y-axis). Expression values are based on normalized counts (NC). (C) Differentially accessible regions (DARs) identified using assay for transposase accessible chromatin (ATAC)-seq ( $FDR < 10 %$ , $300 bp$ windows) exhibit distinct profiles in CAST/EiJ and C57BL/6J. Hierarchical clustering of samples is represented by a dendrogram. (D) Representative loci for DARs (asterisks) between CAST/EiJ control and C57BL/6J control.

Figure 1A is a bubble plot. Figure 1B is a scatter plot with a reference line for which x=y, to represent a fold change of zero. Figure 1C is a heat map of differentially accessible regions of CAST/EiJ and C57BL/6J mice, along with a dendogram. The mean-centered normalized chromatin accessibility ranges from negative 3 to 3. Figure 1D shows sequence reads of representative loci Exo1, and Rbck1 and Trib3 in CAST/EiJ and C57BL/6J mice. — Strain-specific transcriptome dynamics, microRNA (miRNA) profiles, and chromatin accessibility in the mouse lung without exposure to 1,3-butadiene. (A) Bubble plot showing enriched reactome pathways for differentially expressed genes more highly expressed in CAST/EiJ control mice compared with those more highly expressed in C57BL/6J control mice. For each pathway, significance is represented by shading, and the number of genes in each pathway is represented by bubble size. For clarity, groups of related pathways are labeled with a general descriptive term as opposed to individual pathway names. A false discovery rate $(FDR) of < 10 %$ was used to determine significance, but owing to the number of significant pathways, only the top 105 pathways in either direction are shown (see Excel Table S3 for a complete list). (B) Average expression of miRNAs in CAST/EiJ control (x-axis) compared with C57BL/6J control (y-axis). Expression values are based on normalized counts (NC). (C) Differentially accessible regions (DARs) identified using assay for transposase accessible chromatin (ATAC)-seq ( $FDR < 10 %$ , $300 bp$ windows) exhibit distinct profiles in CAST/EiJ and C57BL/6J. Hierarchical clustering of samples is represented by a dendrogram. (D) Representative loci for DARs (asterisks) between CAST/EiJ control and C57BL/6J control.