Fig. 3: Dynamics and differentiation trajectories of intestinal stem cell (ISC) subsets in irradiation-induced intestinal injury and regeneration.
From: Single-cell map of dynamic cellular microenvironment of radiation-induced intestinal injury
a tSNE projection of 2,411 ISCs identified, colored by Seurat cluster identities. b Heatmap of the average expression of the selected ISC function-related marker genes in five ISC clusters. c Dot plots showing the ratio of observed to expected cell numbers (RO/E) of each ISC cluster in the indicated samples, with log-transformed Bonferroni-corrected P values in Chi-square tests. d Line charts showing the average luminous density of Olfm4 in immunostaining (blue) and the fraction of Olfm4+ CBCs (clusters 4, 9 and 16; red) in the indicated groups. e Olfm4 immunostaining (red) in jejunum in the control, day 1, 3, 7 and 14 groups. Scale bar = 25 μm. f RNA velocities of ISCs from the control and day 1 groups visualized on the tSNE projection. g The same as (f) for ISCs from the day 1 and day 3 groups. h Heatmap depicting the estimated activity of top 15 regulons showing differential activation in ISCs along the velocity flow from the control and day 1 groups, which is depicted by a black dashed line in (f). Shown are normalized mean area under the curve (AUC) scores of expression regulation by each transcription factor estimated in SCENIC. Cells are ordered according to first principal component (PC1) coordinate to grasp the primary velocity orientation. i, j The same as (h) for ISCs along the velocity flow from the day 1 and day 3 groups, which is depicted by black dashed lines in the left (i) and right (j) panel in (g).
