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Fig. 2 | Genome Medicine

Fig. 2

From: Development of double-positive thymocytes at single-cell resolution

Fig. 2

Single-cell ATAC-seq revealed new transcription factors involved in thymocyte development. a Heat map of dynamically changing genes during thymocyte development. Cells (columns) are ordered from DN to SP, as predicted by PBA. Genes (rows) are ordered by smoothed peak expression using a Gaussian kernel. b Dynamic TF enrichment during thymocyte development, as predicted by SCENIC. Clusters are as labeled in Fig. 1b. The color bar represents the average of the TF enrichment score for each stage. TFs in red were reported to be essential for the development of thymocytes in previous studies. c scATAC-seq data were mapped onto scRNA-seq data (see “Methods”). d Enrichment of TFs (E2f1, Rorc, Srf and Egr3) during thymocyte development (see “Methods”) in scATAC data. The color bar represents the deviation in TFs. Each dot represents one cell. e Circos plot describing the regulation of genes by TFs. The left side shows the TFs enriched at each stage (colors correspond to DN, ISP, DPbla, DPre, DPsel, CD4sp, CD8sp), as shown in Fig. 2b. The right side shows genes differentially expressed at each stage, as in Fig. 2a; some marker genes at each stage are marked outside the circle. The line from left to right indicates that the TFs regulate corresponding genes. The gray link indicates that the correlation between TFs and genes is less than 0.4

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