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Fig. 4 | Genome Biology

Fig. 4

From: APEC: an accesson-based method for single-cell chromatin accessibility analysis

Fig. 4

APEC accurately identified cell subtypes based on scATAC-seq data from Mus musculus thymocytes. a Experimental workflow of the fluorescent tagmentation- and FACS-sorting-based scATAC-seq strategy (ftATAC-seq). b Indexed sorting of double-negative (DN), double-positive (DP), CD4+ single-positive (CD4SP), and CD8+ single-positive (CD8SP) cells with strong tagmentation signals. c The tSNE of thymocyte single-cell ftATAC-seq data based on the accesson matrix, in which the cells are labeled by the sorting index. d Hierarchical clustering of the cell-cell correlation matrix. On the sidebar, each cell was colored by the sorting index. e The accesson-based Louvain method clustered thymocytes into 11 subtypes. DN.A1 (dark green) & A2 (light green), double-negative clusters; DP.A1~A5 and DPsel.A, double-positive clusters; CD8.A1 (dark blue) & A2 (light blue), CD8+ single-positive clusters; CD4.A (purple), CD4+ single-positive cluster. f Average fragment counts of two DN clusters around the marker genes Cd44 and Il2ra. g Differential enrichment of the motifs Runx, Tcf, Rorc, and Nfkb in the cell clusters. hz-score of the Fisher exact test -log(P value) of the common differential genes between the cell clusters from different experiments. The row and column clusters were identified by data from single-cell transcriptome (SMART-seq) and chromatin accessibility (ftATAC-seq) analysis, respectively

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