Figure 3. Chromatin accessibility analysis reveals heterogeneity and delineates the main CD4⁺ T cell differentiation pathways during chronic viral infection. (See also Figure S4 and Table S3).

(A) UMAP of scATAC-seq data of PD1⁺ CD4⁺ T cells on 21 dpi of LCMV-cl13 infection.

(B) UMAP of gene score (accessibility) and gene integration matrix (expression) for Cxcr5, Tcf7, Slamf6 and Tbx21.

(C) Heatmap visualization of marker gene accessibility scores across clusters represented by gene score values.

(D) Heatmap of marker peak scores of 5,227 cis-regulatory elements in scATAC-seq clusters (left). Heatmap of enriched motifs in marker peaks of the specific clusters (right).

(E) UMAP projection of Tfh and Teff differentiation trajectory, respectively. Cells that are not part of the trajectory are colored grey (top). Pseudotime heatmaps of motif deviation scores on the two differentiation trajectories (bottom).

(F) Volcano plot visualization of the differential peak analysis between the indicated clusters (FDR <= 0.1 and a Log₂FC >= 0.5)

(G) Hockey plot representation of the enriched motifs under the cluster specific peak sets.

(H) Pseudotime analysis of the gene scores (accessibility) and gene integration scores (integrated expression values) of the indicated genes.