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README.md

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+# CDT2-data
+
+Data files for [Central Dogma Transformer II (CDT-II)](https://github.com/nobusama/CDT2).
+
+## Files
+
+| File | Description | Size |
+|------|-------------|------|
+| `morris_celllevel_effects_2361.h5` | Cell-level perturbation effects (TSS, 2,361 genes) | 41 MB |
+| `morris_snp_celllevel_effects_2361.h5` | Cell-level perturbation effects (SNP, 2,361 genes) | 34 MB |
+| `k562_gene_embeddings_aligned.h5` | Gene embeddings from scGPT (2,360 genes) | 4.4 MB |
+| `cdt_morris_celllevel_best.pt` | Trained CDT-II model weights | 80 MB |
+
+## Enformer Embeddings (Not Included)
+
+The Enformer embeddings must be generated using the notebooks in the CDT2 repository:
+
+- `morris_28genes_enformer.h5` - Generate with `notebooks/embeddings/Morris_28genes_Enformer.ipynb`
+- `morris_snp_enformer.h5` - Generate with `notebooks/embeddings/Morris_SNP_Enformer.ipynb`
+
+These notebooks run Enformer inference on Google Colab and save the embeddings to Google Drive.
+
+## Usage
+
+```python
+from huggingface_hub import hf_hub_download
+
+# Download cell-level effects
+effects_path = hf_hub_download(
+    repo_id="nobusama17/CDT2-data",
+    filename="morris_celllevel_effects_2361.h5",
+    repo_type="dataset"
+)
+
+# Download model weights
+model_path = hf_hub_download(
+    repo_id="nobusama17/CDT2-data",
+    filename="cdt_morris_celllevel_best.pt",
+    repo_type="dataset"
+)
+```
+
+## Data Source
+
+- Morris STING-seq v2 dataset (60,505 K562 cells, 447 perturbation loci)
+- Reference: [Morris et al. Science 2023](https://www.science.org/doi/10.1126/science.adh7699)
+
+## Citation
+
+```bibtex
+@article{ota2025cdtii,
+  title={Central Dogma Transformer II: An AI Microscope for Understanding Cellular Regulatory Mechanisms},
+  author={Ota, Nobuyuki},
+  journal={bioRxiv},
+  year={2025}
+}
+```
+
+## License
+
+MIT License