longevity-db/Tabula_Muris_Senis_10x

🧬 Tabula Muris Senis – 10x Dataset (Mouse Aging Atlas)

Organism: Mus musculus
Assay: 10x Genomics Single Cell 3' v2
Tissues: 16 mouse tissues (e.g., heart, lung, kidney, liver)
Cells: 245,000+ single cells
Age groups: Spanning mouse lifespan (young to old)

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📖 Dataset Description

This dataset is a subset of the Tabula Muris Senis project, a collaborative effort to create a comprehensive single-cell transcriptomic atlas of aging in the mouse. The 10x portion of the data includes over 245,000 cells across 16 tissues profiled using droplet-based 10x Genomics technology. It provides a powerful resource for understanding how aging affects individual cell types across diverse tissues.

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📂 Files Included

• TMS_expression_sparse.parquet – Chunked gene expression matrix (cells × genes)
• TMS_metadata.parquet – Metadata per cell (tissue, age, sex, cell type, etc.)

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🚀 Usage Instructions

import pandas as pd

# Load the expression and metadata files
expression = pd.read_parquet("TMS_expression_sparse.parquet")
metadata = pd.read_parquet("TMS_metadata.parquet")

# Optionally merge for analysis
df = expression.join(metadata)

Alternatively, load from Hugging Face:

from datasets import load_dataset

ds = load_dataset("longevity-db/tabula-muris-senis-10x")
df = ds["train"].to_pandas()

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💡 Use Cases

• Transcriptomic Aging Analysis: Discover how aging influences gene expression across cell types and tissues.
• Cross-Tissue Comparisons: Study systemic versus tissue-specific aging trajectories.
• Biological Age Modeling: Train machine learning models to predict biological age from transcriptomic signatures.
• Single-Cell Method Development: Benchmark algorithms for clustering, integration, or trajectory inference on aging data.
• Sex-Specific Aging Research: Explore differences in aging across male and female samples.
• Cross-Species Comparisons: Integrate this dataset with human aging data to identify conserved mechanisms.

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📚 Citation

If you use this dataset, please cite the original publication:

Tabula Muris Consortium (2020).
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse.
Nature, 583, 590–595.
https://doi.org/10.1038/s41586-020-2496-1

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🙏 Acknowledgments

This dataset was produced by the Tabula Muris Consortium, made possible by the Chan Zuckerberg Biohub and the CZI Initiative.
The data was accessed via cellxgene.cziscience.com and reformatted by Iris Lee for easier community use. ### 🧑‍💻 Team: MultiModalMillenials. Iris Lee (@iris8090)

We acknowledge the developers of open-source tools such as scanpy, anndata, pandas, and pyarrow that made processing and sharing this dataset possible.

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