ArticleiScience2023
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery.
Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Synchronization of the 12-h circatidal rhythm maintains the kidney through repeated cycles of warm reperfusion in the hibernating ground squirrel.Function (Oxford, England) · 2026Article
- Robust semi-supervised scRNA-seq integration from virtual adversarial learning.bioRxiv : the preprint server for biology · 2026Article
- Insulin receptorNature communications · 2026Article
- Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Article
- Spatial single cell transcriptomic analysis informs tumor developmental hierarchy of DICER1 syndrome related sarcoma.Nature communications · 2026Article
- A benchmark of semi-supervised scRNA-seq integration methods in real-world scenarios.PLoS computational biology · 2026Article
- BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration.PLoS computational biology · 2026Article
- AZGP1 deficiency promotes chronic kidney fibrosis in aging mice.American journal of clinical and experimental urology · 2026Article
- Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets.Computational and structural biotechnology journal · 2026Article
- Article
- A comparative review of single-cell atlases: mapping cellular diversity across species and tissues.Cellular and molecular life sciences : CMLS · 2025Review
- HIFα isoform specific activities drive cell-type specificity of VHL-associated oncogenesis.Nature communications · 2025Article
- Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases.Nature aging · 2025Article
- Lack of a role of NHE4 in renal ammonia metabolism.American journal of physiology. Renal physiology · 2025Article
- Article
- Considerations for building and using integrated single-cell atlases.Nature methods · 2025Review
- High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.Scientific reports · 2024Article
- High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction.BMC genomics · 2024Article
- Cytochrome bAging cell · 2024Article
- High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The kidney's cellular diversity is on par with its physiological intricacy; yet identifying cell populations and their markers remains challenging. Here, we created a comprehensive atlas of the healthy adult mouse kidney (MKA: Mouse Kidney Atlas) by integrating 140.000 cells and nuclei from 59 publicly available single-cell and single-nuclei RNA-sequencing datasets from eight independent studies. To harmonize annotations across datasets, we built a hierarchical model of the cell populations. Our model allows the incorporation of novel cell populations and the refinement of known profiles as more datasets become available. Using MKA and the learned model of cellular hierarchies, we predicted previously missing cell annotations from several studies. The MKA allowed us to identify reproducible markers across studies for poorly understood cell types and transitional states, which we verified using existing data from micro-dissected samples and spatial transcriptomics.
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