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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation

Fig. 4

Association of differentially accessible regions with altered gene expression between C57BL/6J and A/J. A Differential peaks are highly associated with differential genes. Top differential peaks (labelled as red) are defined by Wilcoxon rank-sum test with FDR < 0.05 within top 1% of logFC. The read counts in peaks of snATAC-seq bulk are log10-transformed. Peaks with low read count (less than median—1.5 median absolute deviation) are filtered out. To associate differential peaks to DEGs, peaks are overlapped with the regulatory region of DEGs (basal region ± 100 kb until nearby genes). As a control, random peaks are selected by bootstrapping with 1000 repetitions (p < 0.0099). The RPKM from bulk RNA-seq of C57BL/6J and A/J (n = 12 per strain) is also log10-transformed, and DEGs are defined as FDR < 0.05 and log2-fold change > 1 (labelled as red). B Cell-type-specific differential peaks correlate with gene expression in bulk RNA-seq. The differential peaks are labelled as green. *FDR < 0.05

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