Single-cell atlas of human kidneys in health, chronic kidney disease and transplant rejection

This single-cell RNA-sequencing (scRNA-seq) dataset comprises two files: an RData file (combined_data.RData), which can be loaded into RStudio to generate a Seurat object, and an h5ad object (annotated_combined_adata_full.h5ad) for downstream analysis in Scanpy or cellxgene.

The dataset contains previously published data and five new samples derived from kidney allografts undergoing graft nephrectomies. Overall, 217,411 human kidney cells are included, including 151,038 ‘control’ cells from living donor biopsies or non-tumorous regions of tumour nephrectomies and 66,373 cells from diseased samples, including chronic kidney disease and different aetiologies of transplant rejection.

For full information on generation of the dataset, please see the associated preprint, which has been uploaded to bioRxiv and is available at: https://www.biorxiv.org/content/10.1101/2022.10.28.514222v2. The code used for scRNA-seq analysis is available at: https://github.com/daniyal-jafree1995/kidney-lymphatics/blob/master/Jafree_2023_JCI_analysis.R.