Fig. 3. Nur77-GFP^HI and Nur77-GFP^LO CD4 T cells differ in expression of effector molecules.

a–d Single-cell RNA-Sequencing of Nur77-GFP^LO and Nur77-GFP^HI CD4 T cells (2,664 and 1386, respectively) sorted from Nur77-GFP lungs at four weeks post-infection. a Data show paired cells from an individual mouse, representative of 4 biological replicates. Colors indicate transcriptomic clusters with manual annotation based on differential expression of marker genes. b Feature plots show regions of elevated expression of indicated genes in Nur77-GFP^LO and Nur77-GFP^HI cell populations. For IV label, CD45.2 CITE-seq antibody was injected immediately before harvest. c Dot plots show relative abundance (color scale) and prevalence (circle size) of indicated gene expression in each cluster, in Nur77-GFP^LO and Nur77-GFP^HI cell populations. Source data for a–c are located in Supplementary Data S3d Columns indicate percent of Nur77-GFP^LO and Nur77-GFP^HI CD4 T cells expressing each gene, paired from 4 individual mice. Asterisks indicate q value < 0.05 for paired two-tailed t tests adjusted for multiple comparisons, with precise q value listed in Supplementary Data S4. e Flow cytometry of OX40 surface protein expression on Nur77-GFP^LO and Nur77-GFP^HI CD4 T cells from Nur77-GFP lungs harvested at four weeks post-infection. CD45.2 fluorescent antibody injected immediately before harvest identifies vascular cells. Tetramer⁺ cells represent either Ag85B or ESAT-6 specificity. Gated on IV^- Tetramer⁺ or bulk live CD4⁺ CD44⁺ Nur77-GFP^LO or Nur77-GFP^HI cells. P values calculated with a paired two-tailed t-test, 5-6 mice per group. Error bars indicate standard deviation.