GSE208154 – Complete Cell Atlas of Aging C. elegans

📄 Description

This dataset provides a comprehensive single-cell RNA sequencing (scRNA-seq) profile of C. elegans across six adult time points. It is a highly curated developmental and aging atlas, useful for longevity, developmental biology, and transcriptomic studies.

📊 Dataset Summary

• Species: Caenorhabditis elegans
• Type: Single-cell RNA-seq (scRNA-seq)
• Samples: 11 GSM samples from GEO
• Format:
  • GSE208154_expression_sparse.parquet: Sparse gene expression matrix
  • GSE208154_metadata.parquet: Cell metadata

📁 Files Included

• GSE208154_expression_sparse.parquet
• GSE208154_metadata.parquet

📥 How to Load

import scipy.sparse
import pandas as pd

# Load expression matrix
X = scipy.sparse.load_npz("GSE208154_expression_sparse.parquet")

# Load metadata
metadata = pd.read_parquet("GSE208154_metadata.parquet")

💡 Use Cases

• Aging research in model organisms
• Cell type classification and developmental biology
• Benchmarking unsupervised and supervised learning on scRNA-seq data
• Pseudotime or trajectory inference studies

📚 Citation

If you use this dataset, please cite:

Lipinszki, Z., et al. (2022). A complete single-cell transcriptomic atlas of aging C. elegans. Nature Aging, DOI: 10.1038/s43587-022-00217-x

🙏 Acknowledgments

We thank Calico Life Sciences for generating and sharing this valuable resource and NCBI GEO for providing public access.

Curated and converted by Iris Lee-participant of the Longevity Hackathon 2025.