Fig. 6: Analysis of the chromatin state of TEs in single-cell ATAC-seq data. | Nature Communications

Fig. 6: Analysis of the chromatin state of TEs in single-cell ATAC-seq data.

From: Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

Fig. 6

a Schematic plot of scTE for scATAC-seq data analysis. The reads are mapped to the genome, and assigned to a metagene TE, and then the cells were clustered based on the TE matrix. b UMAP plot of the TE chromatin state from scATAC-seq data for a selection of FACS-purified mouse cell types. c Heatmap of the top 50 cell type-specific opened TEs in the indicated cell types, selected example TEs are indicated. d UMAP plot as in (b), but cells are colored by chromatin-state of the indicated TEs. e Genome tracks showing the aggregate scATAC-seq profiles (top panel). Randomly selected 100 single cell profiles are show below the aggregated profiles (bottom panel). Which include (unique + multiple), or exclude (unique), multiple mapped reads. f UMAP plot of the expression of the myocardium marker gene Smyd1, from the cardiogenesis data, see Fig. 3i.

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