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Fig. 1 | BMC Biology

Fig. 1

From: Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

Fig. 1

Single-cell ATAC-seq and cluster annotation of rice root tips. a Schematic overview of the experimental workflow. b UMAP visualization of nine clusters of root tip cells. Each dot indicates a single cell. Colours in the diagram of the root tip indicate the corresponding cell type. c Enrichment of accessibility of proximal regulatory elements for marker genes as identified by single-cell RNA-seq. Dot diameter, proportion of cluster cells with proximal regulatory elements for a given gene; colour, mean accessibility across cells in that cluster. d UMAP visualization of cell type-specific gene accessibility for a subset of marker genes associated with six different cell types. Each dot indicates a single cell. e Cluster-aggregated chromatin accessibility surrounding the gene LOC_Os01g15610 for cells of endodermis. f RNA in situ hybridization of cell type accessibility marker gene LOC_Os04g53640 for rice root cap. Scale bar, 40 μm. g UMAP visualization of cell type-specific gene accessibility of LOC_Os04g53640 for rice root cap. Each dot indicates a single cell. h Scatter plots of GO enrichment analysis of differentially accessible genes for each cluster. Overrepresentation analysis and visualization performed using the ClusterProfiler R package. GO terms were obtained with adjusted p-value < 0.05 using the Benjamini–Hochberg method

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