Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development

Copyright and License

© 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Data Availability

Single cell/nuclear RNA-seq and ATAC-seq data have been deposited at Gene Expression Omnibus and are publicly available as of the date of publication. Accession numbers are listed in the key resources table.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Code Availability

All original code has been deposited on GitHub (Zenodo archive: https://doi.org/10.5281/zenodo.11521216).

Acknowledgement

Work in A.P.M.’s laboratory was partially supported by grants DK054364, an RBK partnership grant DK126024, and CZI grant WU-20-101 as part of the Seed Network of the Human Cell Atlas consortium (HCA).

Contributions

A.P.M. conceived the study. K.K. performed single-cell data collection. S.K., R.K.P., M.A., and J.S. designed and/or analyzed data in consultation with A.P.M. and N.O.L. J.G. and S.K. performed secondary verification and followed up on studies of single-cell data predictions. S.K. assembled figures. S.K. and A.P.M. wrote the manuscript, incorporating comments from all authors.

Conflict of Interest

A.P.M. is a consultant or scientific advisor to Novartis, eGENESIS, Trestle Biotherapeutics, GentiBio, and IVIVA Medical.

Supplemental Material

• Document S1. Figures S1–S6.
• Table S1. Complete list of human and mouse developmental sc/snRNA-seq and snATAC-seq sequencing data used in this study, related to Figures 1 and S1.
• Table S2. Human and mouse global and N-UE sub-clustering sc/snRNA-seq and snATAC-seq data lists of differentially expressed genes (RNA) and differentially accessible regions/differential TF binding predictions (ATAC) for each cluster shown in the UMAP projections in Figures 1B, 1C, 1F, 1G, 2B, 2C, and 2K–2O, related to Figures 1, 2, S1, and S2. See tab entitled “Readme” for key to content, Excel file.
• Table S3. Human and mouse PAX8/Pax8-expressing differentiating nephrons and three lineage specification trajectory data list of differentially expressed genes shown in the UMAP projections in Figure 3B, related to Figures 3 and S3. See tab entitled “Readme” for key to content, Excel file.
  Table S4. Cross-species pseudo-multimodal integrated N-UE datasets list of differentially expressed genes (RNA) and differentially accessible regions/differential TF binding predictions (ATAC) for each cluster shown in the UMAP projections, related to Figures 4 and S4. See tab entitled “Readme” for key to content, Excel file.
• Table S5. Conserved and human-specific differentially expressed genes and differentially accessible regions for each corresponding human/mouse sc/snRNA-seq or snATAC-seq clusters in the integration analysis in Figure 4A, related to Figures 4, 5, 6, and S4. See tab entitled “Readme” for key to content, Excel file.
• Table S6. Mouse stage-specific differentially expressed genes among the E15.5, E17.5, and P0 kidney, related to Figures 4, 5, 6, and S4. Mouse stage-specific differentially expressed genes among the E15.5, E17.5, and P0 kidney scRNA-seq datasets from Naganuma et al. (2021).
• Table S7. Genes with distinct local enrichment patterns in the integration analysis in Figure 4A, related to Figure 5.
• Table S8. Highly correlated open chromatin regions to gene expression and cross-reference analysis with the EBI GWAS SNP data in the human N and UE cell-type clusters of the integrated cross-species pseudo-multimodal datasets, related to Figures 7 and S6.
• Document S2. Article plus supplemental information.