Fig. 2: Single-nucleus RNA and ATAC joint profiling from human kidney mini biopsies.

a, A total of 25 renal biopsy samples from patients with kidney disease and 10 healthy control samples from kidney transplantation donors were utilized for Multiome UDA-seq analysis. b, A schematic of the joint snATAC-seq and snRNA-seq analysis for kidney biopsy samples. c, The data quality of the Multiome UDA-seq, showing the distributions of gene number per cell (top left) and FiRP per cell (top right) for patients with disease (n = 25) and healthy control donors (n = 10). Box plots show interquartile range with the median marked. The whiskers extend up to 1.5 times the interquartile range, and the outliers are not displayed. Bottom left: normalized insertion profile around transcriptional start sites for patients with disease and healthy donors. Bottom right: the length distribution of fragments from patients with disease and healthy donors. d, UMAP plots with cells colored by clusters, defined by snRNA-seq alone (top) or snATAC-seq alone (bottom). e, A dot plot showing differentially expressed genes across the major cell types. f, A track plot showing differentially accessible regions across the major cell types. g, UMAP plots with cells colored by clusters, defined by weighted nearest network joint analysis of snRNA-seq and snATAC-seq. h, Peak2Gene links (P2GLinks) in kidney snRNA-seq and snATAC-seq profiles shown in a heat map with 25 modules. Each row represented a single cell, grouped by its cell type. Panel b was created using BioRender.com. Full names for all abbreviations of cell types in panels d–h can be found in the Methods.