Supplementary Figure 3: Focused analysis of kidney myeloid cells.

a, The expression of selected genes over the 5 myeloid cell clusters. b-c, The expression of the canonical markers CD16 (FCGR3A) and CD14 on the 5 myeloid clusters. d-f, The changes in the expression of 3 selected genes, along the trajectory from CM0 to CM4; ‘pseudotime’ represents the ordering of the cells along this trajectory. The violin plots (shades) show the distribution of expression levels in equally-spaced intervals along the pseudotime axis (and do not directly correspond to cell clusters). g, The scRNA-seq data of myeloid blood cells sorted from 2 LN patients, projected in the tSNE plane. Low-resolution clustering identified a cluster of CD16⁺ monocytes; other myeloid cells are grouped here into an ‘other’ set. h, The results of comparing the blood CD16⁺ monocytes to the 5 myeloid cells clusters found in kidney (CM0-CM4). For each blood cell, the most similar kidney cluster was determined; the bar plot denotes the percentage of myeloid cells most similar to each of the kidney myeloid clusters (only values larger than 0 are shown). i, The increase in the phagocytosis score, computed as the average expression of several genes associated with phagocytosis, in cluster CM1 compared to cluster CM0, in blood myeloid cells. j, Same as (i), but with regard to kidney myeloid cells. ***—p-value < 0.001 (two-tailed Mann-Whitney U-test).