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--- |
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license: cc-by-4.0 |
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tags: |
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- biology |
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dataset_info: |
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features: |
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- name: counts |
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sequence: int32 |
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- name: counts_norm |
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sequence: float32 |
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- name: counts_log |
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sequence: float32 |
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- name: counts_log_norm |
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sequence: float32 |
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- name: gene_names |
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sequence: string |
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- name: control_counts |
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sequence: float32 |
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- name: control_counts_norm |
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sequence: float32 |
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- name: control_counts_log |
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sequence: float32 |
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- name: control_counts_log_norm |
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sequence: float32 |
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- name: delta_counts |
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sequence: float32 |
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- name: delta_counts_norm |
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sequence: float32 |
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- name: delta_counts_log |
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sequence: float32 |
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- name: delta_counts_log_norm |
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sequence: float32 |
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- name: cell_line |
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dtype: string |
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- name: perturbation |
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dtype: string |
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- name: compound_concentration |
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dtype: float64 |
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- name: compound_unit |
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dtype: string |
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- name: compound_smiles |
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dtype: string |
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- name: mechanism |
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dtype: string |
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- name: moa |
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dtype: string |
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- name: biological_effect |
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dtype: string |
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- name: experimental_id |
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dtype: string |
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- name: timepoint |
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dtype: string |
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- name: text |
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dtype: string |
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- name: text_embeddings |
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sequence: float32 |
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- name: chembert_embeddings |
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sequence: float32 |
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splits: |
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- name: train |
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num_bytes: 84911752257 |
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num_examples: 24262 |
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download_size: 12664654443 |
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dataset_size: 84911752257 |
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configs: |
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- config_name: default |
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data_files: |
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- split: train |
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path: data/train-* |
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--- |
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## Dataset Description |
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**A549 Chemical Perturbation Dataset (SciPlex2)** |
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This dataset captures transcriptional responses of **A549**, a human lung adenocarcinoma cell line, to drug perturbations. Cells were treated with one of four small molecules: |
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- **Dexamethasone**, corticosteroid receptor agonist |
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- **Nutlin-3a**, p53-MDM2 interaction antagonist |
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- **BMS-345541**, inhibitor of NF-κB–dependent transcription |
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- **Vorinostat (SAHA)**, histone deacetylase (HDAC) inhibitor |
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Each compound was applied for **24 hours** across **seven doses**, in **triplicate**, resulting in **84 compound–dose–replicate conditions**, along with additional vehicle controls. Single-cell transcriptional profiles were generated using **sci-RNA-seq**. |
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## Additional Information |
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- **Normalized counts** were scaled so that the total expression per cell sums to `1e4`. |
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- **Control counts** represent the average expression of each gene across all control cells. |
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- **Delta values** are computed as the difference between each sample's expression and the corresponding control mean. |
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- **SMILES** strings and **mechanism of action (MoA)** annotations were retrieved from the [ChEMBL](https://www.ebi.ac.uk/chembl/) database and enhanced with additional sources. |
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## Citation |
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> Srivatsan, S. R., McFaline-Figueroa, J. L., Ramani, V. *et al.* |
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> **Massively multiplex chemical transcriptomics at single-cell resolution** |
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> *Science*, **367**, 45–51 (2020). |
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> [https://doi.org/10.1126/science.aax6234](https://doi.org/10.1126/science.aax6234) |
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