Fig. 3: Transcriptional trajectories in NeuMap.
a–c, K-mass score (representing cell density) of neutrophils from the bone marrow, blood, spleen, lungs and livers of naive mice (a), tumour-bearing mice (PDAC tumours) (b) and LPS-treated mice (c), projected onto NeuMap. RNA velocity analyses were performed for each of the conditions and the main developmental trajectories are highlighted with red arrowheads. d, K-mass score of the mapped time-stamped neutrophils from steady-state, inflammation (LPS) and tumour-bearing (LLC) mice onto NeuMAP. Neutrophils were tracked at 24 h (bone marrow, black dots), 36 h and 72 h (blood, spleen and lung, orange-red scale) after tamoxifen-induced labelling of Ly6g-tdTomato cells. e, Network model highlighting the trajectories identified in a–d, showing genes and transcription factors enriched for each trajectory. Transcription factors were selected when identified by both EnrichR and chromatin accessibility analyses. Note that we did not find any transcription factor enriched in the immuno-silent path. For a complete list see Supplementary Table 7. f, Inference of preferred trajectories for neutrophils from healthy, tumour-bearing and inflamed mice from the data in a–d.
