Fig. 1: Inflammation landscape of circulating immune cells.

a, Left, schematic overview illustrating the number of cells, samples and conditions (diseases and disease groups) analyzed. Right, pie charts displaying metadata related to the scRNA-seq chemistry (10x Genomics assay and version) and patient demographics (age and sex). b, Schematic overview of the analysis workflow followed, detailing the division of the overall dataset into Main, unseen patients and unseen studies. The figure illustrates the specific tasks and analyses performed with each dataset. c, Uniform manifold approximation and projection (UMAP) embedding for the scANVI-corrected latent space considering the Main dataset (4,435,922 cells) across patients and diseases colored by the major cell lineages (top, Level 1) and diseases (bottom). d, Sankey diagram showing the Inflammation Atlas cell annotation, considering major cell lineages (Level 1, left) and cell type populations (Level 2, right), along with their correlation to Level 1 cell groups. a,b, Icons were created in BioRender: Aguilar Fernandez, S. (2025): https://biorender.com/h7jfeqm or with Inkscape. CM, central memory; D, disease; DC, dendritic cell; DEG, differentially expressed genes; EM, effector memory; HC, healthy control; HVG, highly variable genes; Mono, monocytes; NK, natural killer; pDC, plasmacytoid dendritic cell; QC, quality control.