CellCarto Cold Ischemia Timecourse

Interactive web application and data resource for exploring spatiotemporal transcriptomic changes in murine kidneys during cold ischemic injury.

The app supports compartment-specific exploration of spatial transcriptomics data across cold ischemia timepoints, with views for cortex, outer medulla, and inner medulla responses.

Links

• Web app: https://jef.works/CellCarto-ColdIschemia/
• Manuscript: https://www.biorxiv.org/content/10.1101/2025.05.25.654911v2
• Repository: https://github.com/JEFworks-Lab/vitessce-cold-ischemia

Features

• Interactive spatial and harmonized t-SNE views of murine kidney spots.
• Gene search and gene-expression coloring.
• Filters for metadata-driven exploration.
• Adjustable point size, sampling, color palettes, and light/dark theme.
• Timecourse plots for selected genes across kidney compartments.
• Gene tables for compartment-specific upregulated and downregulated gene sets.
• Static GitHub Pages build in docs/.

Data

The data/ directory contains the processed data used by the browser:

• cold_ischemia_union.zarr/: unified AnnData/Zarr dataset for app rendering.
• CI_cells_*.json: spatial spot/cell-level data by compartment and regulation direction.
• CI_clusters_*.json: gene-expression matrices for compartment-specific gene sets.
• CI_cell_sets_*.json: gene-set membership files.
• CI_timecourse_*.json: average gene-expression timecourse data.
• CIS_All_DEGs_Slope_R2_by_section.json: slope and R2 summaries by kidney section.
• harmonized_tsne_embeddings.json: harmonized t-SNE coordinates.

Timepoints represented in the app include 0, 12, 24, and 48 hours of cold ischemia.

Repository Structure

.
├── data/       Processed JSON and Zarr data used by the app
├── docs/       Production build for GitHub Pages
├── public/     Static public assets copied into builds
├── R/          Early R/Vitessce workflow notes
├── scripts/    Data conversion and asset-copy helper scripts
└── src/        React landing page and D3/Three.js app source

Local Development

Install dependencies once:

npm install

Run the app locally:

npm start

The development server opens at http://localhost:3000.

Build for GitHub Pages

Build the production app:

npm run build

Replace the GitHub Pages build directory:

rm -rf docs
mv build docs

The prestart and prebuild scripts run scripts/copy-d3-assets.js so the standalone D3 app assets are available to React and the static build.

Data Conversion

The unified Zarr dataset can be regenerated from the processed JSON files with:

python scripts/convert_unified_zarr.py

See the script docstring and arguments for conversion details.

Citation

If you use this app, code, or processed data, please cite the associated manuscript and the archived GitHub/Zenodo release DOI for the version used.

Singh S, Patel SK, Matsuura R, Velazquez D, Sun Z, Noel S, Rabb H, Fan J.
Spatiotemporal Transcriptomic Analysis of the Murine Kidney Reveals
Compartment-Specific Changes During Cold Ischemic Injury.
bioRxiv. 2025.

Dee Velazquez, & Jean Fan. (2026). JEFworks-Lab/CellCarto-ColdIschemia: v1.0.0 - Initial Release (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.20417220

License

This repository is released under the MIT License. See LICENSE for details.