---
license: cc-by-4.0
tags:
- biology
dataset_info:
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    sequence: int32
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  - name: delta_counts_log_norm
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  - name: cell_line
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  - name: perturbation
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  - name: compound_concentration
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  - name: compound_unit
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  - name: compound_smiles
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  - name: mechanism
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  - name: chembert_embeddings
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  splits:
  - name: train
    num_bytes: 84911752257
    num_examples: 24262
  download_size: 12664654443
  dataset_size: 84911752257
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
---

## Dataset Description

**A549 Chemical Perturbation Dataset (SciPlex2)**

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:

- **Dexamethasone**, corticosteroid receptor agonist  
- **Nutlin-3a**, p53-MDM2 interaction antagonist  
- **BMS-345541**, inhibitor of NF-κB–dependent transcription  
- **Vorinostat (SAHA)**, histone deacetylase (HDAC) inhibitor  

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**.

## Additional Information

- **Normalized counts** were scaled so that the total expression per cell sums to `1e4`.
- **Control counts** represent the average expression of each gene across all control cells.
- **Delta values** are computed as the difference between each sample's expression and the corresponding control mean.
- **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.


## Citation

> Srivatsan, S. R., McFaline-Figueroa, J. L., Ramani, V. *et al.*  
> **Massively multiplex chemical transcriptomics at single-cell resolution**  
> *Science*, **367**, 45–51 (2020).  
> [https://doi.org/10.1126/science.aax6234](https://doi.org/10.1126/science.aax6234)