PLIER latent variable (LV) analysis identifies conserved acute exercise responses across both RNA-seq and ATAC-seq data in slow, fast, and intermediate fiber types. Two LVs representing patterns of upregulation, LV9 (A,B), and downregulation, LV12 (C,D), conserved across both gene expression and promoter chromatin accessibility are shown. For complete PLIER LV analysis, see Supplemental Figure S5. (A,C) Heatmaps represent chromatin accessibility and gene expression z-scored pseudobulk values for the top 30 genes that are associated with each LV. Each column represents one fiber-type sample; columns are ordered by -ome type, exercise group, and time point. Annotation bars on the left side of heatmap show whether genes belong to the delineated pathway. (B,D) Scatterplots represent the summary values for exercise-regulated LVs. Plots are faceted by -ome type (RNA vs. ATAC), exercise group (exercise vs. circadian control), and fiber type. Change between pre- and post-LV summary values is assessed via Holm–Bonferroni adjusted paired t-test with (ns) P > 0.05, (*) P ≤ 0.05, (**) P ≤ 0.01, (***) P ≤ 0.001, and (****) P ≤ 0.0001.
