Article
Extended Data Fig. 6 | Identif ication of gene modules and distribution of
module scores. A total of 162,490 single-cell transcriptomes derived from
unstimulated and PPD-stimulated BAL cells from 15 NHPs (cohort 4, n = 3 per
group) at weeks 13 (peak of BAL response) and 25 (time of challenge) were
profiled. a, Uniform manifold approximation and projection (UMAP) plots of
BAL cells at weeks 13 and 25 after BCG immunization, coloured by time point
(top left), PPD stimulation condition (top right), and cell type (week 13, bottom
left; week 25, bottom right). b, Gene–gene correlation heat map showing
significant gene modules (M1–M7; top) identified among week 13 stimulated
BAL T cells with select genes (right) highlighted. c, t-Distributed stochastic
neighbour embedding (t-SNE) plots of stimulated BAL T cells from weeks 13
(left) and 25 (right), coloured by vaccine group (top), T cell subtypes (middle),
and module 2-positivity (bottom). d, Histograms of the distribution of module
2 scores by vaccine group (colour) and macaque. Dashed line (placed at two s.d.
above the mean score in the naive controls) indicates the threshold used to call
cells as positive for the module. The percentage module 2-positive is shown for
each NHP.