Datasets:
File size: 3,000 Bytes
d3e1e0b c5ff05f 5e8d214 c5ff05f 8653e39 5e8d214 c5ff05f 5e8d214 8653e39 c5ff05f 8653e39 c5ff05f b7b6468 8c70998 5d06e7d 8c70998 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 |
---
license: cc-by-4.0
tags:
- biology
dataset_info:
features:
- name: counts
sequence: int32
- name: counts_norm
sequence: float32
- name: counts_log
sequence: float32
- name: counts_log_norm
sequence: float32
- name: gene_names
sequence: string
- name: control_counts
sequence: float32
- name: control_counts_norm
sequence: float32
- name: control_counts_log
sequence: float32
- name: control_counts_log_norm
sequence: float32
- name: delta_counts
sequence: float32
- name: delta_counts_norm
sequence: float32
- name: delta_counts_log
sequence: float32
- name: delta_counts_log_norm
sequence: float32
- name: cell_line
dtype: string
- name: perturbation
dtype: string
- name: compound_concentration
dtype: float64
- name: compound_unit
dtype: string
- name: compound_smiles
dtype: string
- name: mechanism
dtype: string
- name: moa
dtype: string
- name: biological_effect
dtype: string
- name: experimental_id
dtype: string
- name: timepoint
dtype: string
- name: text
dtype: string
- name: text_embeddings
sequence: float32
- name: chembert_embeddings
sequence: float32
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)
|