Fig. 3

Analysis of the CD7⁺CD3⁻ innate lymphocyte compartment in inflammatory intestinal diseases. a First HSNE level embedding of 5.2 million cells. Color represents arcsin5-transformed marker expression as indicated. Size of the landmarks represents AoI. Blue encirclement indicates selection of landmarks representing CD7⁺CD3⁻ innate lymphocytes and CD4⁺ T cells further discussed in Fig. 5. b The major immune lineages, annotated on the basis of lineage marker expression. c Third HSNE level embedding of the CD7⁺CD3⁻ innate lymphocytes (5.0 × 10⁵ cells). Color represents arcsin5-transformed marker expression in top panels, and tissue-origin and clinical features in bottom panels. Blue encirclement indicates selection of landmarks representing CD127⁺ILC and ILC-like cells. d Third HSNE level embedding shows density features depicting the local probability density of cells, where black dots indicate the centroids of identified cluster partitions using GMS clustering. e Embedding of the CD127⁺ILC and ILC-like cells (6.0 × 10⁴ cells) at single-cell resolution. Arrows indicate ILC1 (blue), ILC2 (orange) and ILC3 (green). Bottom-right panel shows corresponding cluster partitions using GMS clustering based on density features (top-right panel). f A heatmap summary of median expression values (same color coding as for the embeddings) of cell markers expressed by CD127 + ILC and ILC-like clusters identified in b and hierarchical clustering thereof. g Composition of cells for each cluster is represented graphically by a horizontal bar in which segment lengths represent the proportion of cells with: (left) tissue-of-origin, (middle) disease status and (right) sampling status