Figure 5. Age-associated chromatin accessibility and transcriptome pseudotime trajectory analysis.
(A) Heatmap of chromatin accessibility levels for the top 30 genes in the human age-dependent LV (LVageatac).
(B) Cell type and donor color-coding are provided in Figure 4. Additional LV analyses are presented in Figure S4. Plot showing the overall changes in chromatin accessibility for all pituitary cell types over age for females (top) and males (bottom). Pituitary cell types are color-coded, as indicated. Same cell types are connected by lines over donor age.
(C) Chromatin accessibility tracks analysis for ORC4 (left) and EIF4E (right) in all lactotropes in the snATAC-seq datasets from all donors. The gene structure is provided underneath the tracks. Additional tracks are presented in Figure S5.
(D) UMAP showing the trajectory within the stem cell cluster for female (top) and male (bottom) samples, with samples color-coded by age.
(E) Pseudotime trajectory analysis for female (top) and male (bottom) samples. Pediatric PSCs represent the root of each trajectory. The color scale of pseudotime trajectories is displayed.
(F) Gene modules identified with pseudotime and showing expression changes over donor age. Monocle 3 identified sets of genes whose expression changes over donor age as a function of pseudotime. These modules are then plotted on a heatmap to depict their relative expression in each age group. The top three enriched modules for each age group are labeled, with module 1 being the most highly enriched in each age. Pd1-3 denotes the pediatric top three modules, Ad1–3 the Adult-enriched modules, and Ag1-3 the Aged-enriched. Blue to red on the color scale represents low to high relative expression levels (z-transformed mean expression) of gene modules, respectively. See Figure S6 for selected gene trajectories within specific modules. See Table S3B for the top genes per module.