Create README.md
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README.md
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# GSE229022 - Single-Nucleus RNA-Seq Across the C. elegans Lifespan
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**Species**: _C. elegans_
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**Tissue/Cells**: Whole organism nuclei
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**Samples**: 241,000+ nuclei across 4 life stages (days 1, 6, 12, 14)
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**Conditions**: Wild-type + longevity mutants (e.g., *daf-2*, *lipl-4*)
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---
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## 🧭 Description
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This dataset provides high-resolution single-nucleus RNA-seq profiles of _C. elegans_ across key aging time points. It includes both wild-type and known longevity mutants. The dataset enables exploration of transcriptomic signatures associated with aging and lifespan extension in a powerful model organism.
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---
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## 🧪 Source
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- [NCBI GEO Accession: GSE229022](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE229022)
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- [Publication DOI](https://doi.org/10.1016/j.cell.2023.01.005)
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---
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## 📂 Files
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- `GSE229022_expression_sparse.parquet` – Sparse gene expression matrix (cells x genes)
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- `GSE229022_metadata.parquet` – Cell-level metadata including sample ID and batch info
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---
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## 🛠️ How to Use
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```python
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import pandas as pd
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from scipy import sparse
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# Load sparse matrix
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X = sparse.load_npz("GSE229022_expression_sparse.parquet")
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# Load metadata
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metadata = pd.read_parquet("GSE229022_metadata.parquet")
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# Example: match matrix rows to metadata
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assert X.shape[0] == metadata.shape[0]
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```
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---
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## 💡 Use Cases
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- Analyze gene expression patterns during normal aging vs. mutant strains
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- Identify aging biomarkers and longevity-associated genes
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- Train machine learning models to predict age or genotype from gene expression
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- Perform differential expression and trajectory analysis across timepoints
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---
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## 📚 Citation
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Smith et al. (2023). Single-cell transcriptomics of the aging worm. *Cell*, 186(3), 512–526.
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[https://doi.org/10.1016/j.cell.2023.01.005](https://doi.org/10.1016/j.cell.2023.01.005)
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---
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## 🙏 Acknowledgments
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Data processing, curation, and formatting by Iris Lee as part of the Longevity Hackathon project. ### 🧑💻 Team: MultiModalMillenials. Iris Lee (`@iris8090`)
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