Extended Data Fig. 3: Comparison of transcriptional and epigenetic profiles of true naive CD4 T cells with CD4 T cell subsets and across age. | Nature Immunology

Extended Data Fig. 3: Comparison of transcriptional and epigenetic profiles of true naive CD4 T cells with CD4 T cell subsets and across age.

From: Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment

Extended Data Fig. 3

(a) Heatmap of all differentially expression genes (DEGs) using Seurat’s FindAllMarkers function (parameters: logfc.threshold = 0.25, P < 0.05 determined by two-tailed Wilcoxon’s rank sum test) between CD4 T cell subsets in TEA-seq dataset. (b) Heatmap of all differentially accessible peaks using ArchR’s getMarkerFeatures (parameters: FDR< = 0.1, Log2FC ≥ 0.5) between CD4 T cell subsets in TEA-seq dataset. (c) Pseudo-bulk expression values from our confirmatory scRNA-seq dataset from pediatric (Ped), young adult (YA), and older adult naive CD4 T cells of select age-specific genes identified in TEA-seq. (d) Gene expression of SOX4, TOX, CPQ, and STAT4 in bulk-sorted naive CD4 T cells (CD3+CD4+CD8neg CD45RA+CCR7+CD27+CD95neg) from newborn cord blood (n = 7 donors) and older adult peripheral blood (n = 6 donors) using qRT-PCR. Two-tailed Mann-Whitney test. * P < 0.05, **** P < 0.0001. In panels a–c, values have been scaled (z-score) per gene or peak.

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