Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence

Output data and supplementary tables from "Sopena-Rios, M., Ripoll-Cladellas, A. et al. Single-cell analysis of the human immune system reveals sex-specific dynamics of immunosenescence. Nat. Aging (2026). https://doi.org/10.1038/s43587-026-01099-x"

Source Data

01_celltype_proportions_{sex}.rds: Cell type proportions computed at donor level used to run age-compositional analysis (Figure 1e)
02_MiloObject_Preprocessed_{sex}.rds: KNN graph for the differential abundance analysis with Milo (Figure 2a-b)
03_Nhood-cell_id_${sex}.rds: Correspondence of each individual cell to a Milo neighborhood (Figure 2a-b)
04_SO_CD14_Mono_Nhoods_{sex}.rds: Seurat object subsampled for the cells in neighborhoods labeled as CD14 Monocytes (Figure 2f)
05_SO_CD5_Bcells_Nhoods_M.rds: Seurat object subsampled for the cells in neighborhoods labeled as CD5+ B cells in males (Figure 2g)
06_SO_GZMB_CD8TEM_Nhoods_F.rds: Seurat object subsampled for the cells in neighborhoods labeled as GZMB+ CD8 TEM cells in females (Figure 2d-e)
07_Expression_LOESS_{sex}.rds: Normalized expression matrix from non-linear age-DEGs (Figure 3f)
08_Cluster_Loess_expression_{sex}.rds: Clusering of normalized gene expression from non-linear age-DEGs (Figure 3f)
09_SO_CD4TCM_Nhoods_F.rds: Seurat object subsampled for the cells in neighborhoods labeled as CD4 TCM cells in females (Figure 4c)

Supplementary tables

TableS1_CellTypeNames.xlsx: Supplementary table listing immune cell type abbreviations and marker genes used for cell type classification.
TableS2_CellDynamics.xlsx: Supplementary tables providing supporting results for Figure 1 and Extended Data Figure 1, including cell type abundance and age-associated dynamics.
TableS3_DifferentialAbundance.xlsx Supplementary tables providing supporting results for Figure 2 and Extended Data Figure 2, including neighborhood-level differential abundance analyses.
TableS4_DifferentialExpression_linear.xlsx: Supplementary tables providing supporting results for Figure 3 and Extended Data Figures 3 and 4, including sex-stratified differential gene expression analyses.
TableS5_DifferentialExpression_non_linear.xlsx: Supplementary tables providing supporting results for Figure 3 and Extended Data Figure 5, including non-linear age-associated differential gene expression analyses.
TableS6_DiseaseCharacterization.xlsx: Supplementary tables providing supporting results for Figure 6, including disease enrichment and characterization analyses.
TableS7_Milo_subsamplings.xlsx: Supplementary tables providing supporting results for Extended Data Figure 7, including results from Milo downsampling and robustness analyses.