Fig. 1: scRNA-seq analysis of PBMCs from individuals in the S. Typhi human challenge study.
From: Salmonella Typhi gut invasion drives hypoxic immune subsets associated with disease outcomes
a Overview of the study design and cohort for the scRNA-seq experiment: PBMC samples were collected from six individuals in the S. Typhi human challenge study, including three who developed typhoid disease (TD) and three who did not (nTD). Samples were taken at three time points for each individual: before challenge (T0), twelve hours post-challenge (T12h), and at the time of disease diagnosis for TD individuals (TD) or seven days post-challenge for nTD individuals (T7d). b–f tSNE visualization of scRNA-seq data combining all individuals and time points together. Cells are colored by cell type in (b), time point in (c), individual in (d), and disease outcome (nTD or TD) in (e). f tSNE plot from (e), separated to show immune cells from nTD individuals (top) and TD individuals (bottom) alone, highlighting outcome-specific subsets. Cell-type annotations and color legends are provided. g Density plot of iLISI scores for each cell, measuring the degree of mixing across individuals (x-axis) and disease outcomes (y-axis). iLISI scores close to 1 indicate no mixing, while higher scores indicate greater mixing. Three types of immune cell responses are highlighted: 1) Individual-specific responses (iLISI scores close to 1 for both individuals and outcomes mixing), 2) General responses (iLISI scores > 3 for individuals and close to 2 for outcomes), and 3) Outcome-specific responses (iLISI score close to 1 for outcomes and > 2 for individuals).
