Mouse Kidney Atlas (MKA) & MKA-Extended: Single-cell and single-nucleus reference atlases of the mouse kidney

This deposit contains two linked datasets of the mouse kidney: 1. MKA (Mouse Kidney Atlas) A comprehensive reference atlas of the healthy adult mouse kidney, generated by integrating approximately 140,000 cells and nuclei from 59 publicly available single-cell and single-nucleus RNA-sequencing datasets across eight independent studies.The MKA harmonizes annotations through a hierarchical cell-type model, enabling robust cross-study comparisons and accurate labeling of novel or rare cell populations. Original publication: Novella-Rausell et al., iScience (2023). “A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery.” DOI: 10.1016/j.isci.2023.106877 Format: AnnData object (~141,401 observations × 3,000 genes) 2. MKA-Extended An expanded version of the MKA. This extended atlas incorporates immune, injury-induced, and polycystic kidney disease–specific cellular populations, providing a unified reference for Tangram-based deconvolution of spatial transcriptomics datasets. Original publication: Yasinoglu et al., JASN, (2025). “Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease.” DOI: 10.1681/ASN.0000000894 Format: AnnData object (~303,791 observations × 12,156 genes)