Fig. 5: Investigating the PBMC characteristics in an aging female cohort.
a, A flowchart depicting the multimodality experimental design carried out on PBMCs obtained from a female aging cohort, consisting of two batches of donors totaling 10 and 28 individuals, respectively. b, UMAP embedding of 126,616 5′-scRNA-seq profiled PBMC cells, encompassing 27 distinct cell types. c, Aging-related cells detected using SCIPAC with a UMAP visualization with cells color-coded on the basis of the significance of the association, with a red P value indicating a positive association and a blue P value indicating a negative association. The P values were calculated by the SCIPAC nonparametric bootstrap strategy. d, Pie charts showing cell type proportions in age-associated cell groups. Top: age positively associated groups. Bottom: age-negatively associated groups. e, Box plots displaying age-related gene signature scores across different age ranges, indicating a positive association with aging. Box plots show interquartile range with the median marked. The whiskers extend up to 1.5 times the interquartile range. The number of cells for different age ranges is shown at the top of each box plot. f, GO enrichment analysis performed on the gene set forming the age-associated signature. The length of the bars indicates the gene counts for corresponding GO terms, while the colors represent the adjusted P value of enrichment. The P value for GO terms was calculated by the two-sided hypergeometric test and adjusted by the Benjamini–Hochberg method. g, Reclustering of CD4 naive cells, revealing nine subclusters. h, The proportion of CD4 naive subcluster 2 increases with age. i, A stacked violin plot depicting the positive marker genes of subcluster 2 within the CD4 naive population. j, Box plots depicting the TCR clonal diversity across age groups (n = 5, 2, 8, 13 and 10), with each dot representing a donor’s diversity calculated by the inverse Simpson index. The box plots show the interquartile range with the median marked. The whiskers extend up to 1.5 times the interquartile range.
