MLMorizane LabHuman kidney organoids and translational disease modeling

Data Tools

Day64 Kidney Organoid Single-Nucleus Viewer

Interactive UMAP, dot plot, and violin-style expression views for a Day64 kidney organoid single-nucleus RNA-seq atlas containing Control, Cisplatin x3, and Cisplatin x5 nuclei.

Reference UMAP and gene expression

This single-nucleus RNA-seq atlas contains 8,278 nuclei and 33,540 features across Control (4,738 nuclei), Cisplatin x3 (2,534 nuclei), and Cisplatin x5 (1,006 nuclei) conditions.

These plots provide a quick exploratory view of log-normalized nuclear RNA expression. Protein-level validation is strongly encouraged for marker interpretation and biological conclusions.

Injury cluster guide: Injury 1, myofibroblast-like; Injury 2, mixed transitional fibroblast and injured or repairing tubule, with the upper UMAP region leaning fibroblast-like and the lower region leaning repairing-tubule-like; Injury 3, failed-repair tubule-like.

Reference UMAP
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Reference UMAP

Cell type annotation.

Gene UMAP

Enter a gene symbol to color cells by expression.

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Dot plot

Rows are source cell type annotations; columns are conditions. Dot size indicates percent of cells with nonzero expression, and color indicates mean log-normalized expression.

Combined violin

Expression distribution by source cell type, pooling all three conditions.

Source note

Dataset provenance

This exploratory viewer is associated with the kidney organoid injury and repair study by Gupta, Matsumoto, Hiratsuka et al., published in Science Translational Medicine in 2022. Please see the publication for experimental context and interpretation.

Science DOI: 10.1126/scitranslmed.abj4772 | PMC full text: PMC9161367