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Fig. 3 | Genome Medicine

Fig. 3

From: Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis

Fig. 3

Pseudotime analysis reveals distinct trajectories of CD4+ T cell differentiation in vivo. a UMAP plots depicting the inferred diffusion pseudotime of each single cell in the identified T cell clusters. b Graph reconstructing the developmental trajectories between the identified T cell clusters. Edge weights represent confidence in the presence of connections between clusters. The analysis was performed in the combined transcriptional and proteomics data using the partition-based graph abstraction (PAGA) method. ce Reconstructed PAGA paths for the differentiation of the identified Th1 (c), Th17 (d) and Treg (e) lineages. Expression of the lineage-specific transcription factors and selected differentially expressed genes is depicted for each trajectory. f Schematic representation of the identified lineage differentiation trajectories using the single-cell trajectories reconstruction (STREAM) method. Colour code corresponds to the cluster assignment depicted in a. g Expression of the memory-associated CD45RO isoform and the lineage-specific transcription factors TBX21 (encoding TBET), RORC (encoding RORγt) and FOXP3 is depicted along the identified developmental branches

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