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Fig. 6 | Genome Biology

Fig. 6

From: MultiMAP: dimensionality reduction and integration of multimodal data

Fig. 6

Integration of scRNAseq and scATAC-seq data of human fetal thymus reveals transcriptional regulatory principles of T cell development. a MultiMAP visualization of scRNA-seq and scATAC-seq datasets of the human fetal thymus (n = 1), colored by modality and joint clusters identified using the MultiGraph. b Heatmap of gene expression and gene activity scores of key markers of the joint clusters identified using the MultiGraph. c Inferred pseudotime using the MultiGraph recovers the T cell differentiation trajectory. Color indicates pseudotime from red (early, beginning) to blue (late, end). d Heatmap of the gene expression and gene activity scores over pseudotime of genes known to be involved in T cell development. e Smoothed heatmaps of the z-score of the gene expression and motif accessibility of the most variable transcription factors over pseudotime. The motif accessibilities of TFs that varied most in time show changes in accessibility at the transition between the late DN and early DP stage of differentiation. This includes TFs such as GATA3 and LEF1 for which the chromatin at the binding sites closes at that transition, and TFs for which the chromatin at the binding sites opens, such as E2F4, ETS1, and others

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