ArticleSLAS discovery : advancing life sciences R & D2020
Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay.
Article in SLAS discovery : advancing life sciences R & D, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed.
- Review
- Analyzing Cell Painting PLUS Data Using Cell Profiler and KNIME Analytics Platform.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Joint profiling of cell morphology and gene expression during in vitro neurodevelopment.eLife · 2025Article
- Assessing the impact of in vitro xenobiotic metabolism on estrogenic chemical bioactivity in high-throughput profiling assays.Toxicology · 2025Article
- Smaller scale, same impact: replicating high-throughput phenotypic profiling in a medium-throughput lab for use in chemical risk assessment.Archives of toxicology · 2025Article
- Big data and AI: Potential and challenges for digital transformation in toxicology.Environmental analysis, health and toxicology · 2025Article
- Morphological profiling data resource enables prediction of chemical compound properties.iScience · 2025Article
- Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles.Nature communications · 2025Article
- Bioactivity of the ubiquitous tire preservative 6PPD and degradant, 6PPD-quinone in fish- and mammalian-based assays.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Review
- Cell Painting: a decade of discovery and innovation in cellular imaging.Nature methods · 2025Review
- Article
- SPACe: an open-source, single-cell analysis of Cell Painting data.Nature communications · 2024Article
- Cross-Species Molecular Docking Method to Support Predictions of Species Susceptibility to Chemical Effects.Computational toxicology (Amsterdam, Netherlands) · 2024Article
- A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.bioRxiv : the preprint server for biology · 2024Article
- Article
- Applying Cell Painting in Non-Tumorigenic Breast Cells to Understand Impacts of Common Chemical Exposures.bioRxiv : the preprint server for biology · 2024Article
- CRISPRi: a way to integrate iPSC-derived neuronal models.Biochemical Society transactions · 2024Review
- Unleashing the potential of cell painting assays for compound activities and hazards prediction.Frontiers in toxicology · 2024Review
- Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis.Chemical research in toxicology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Cell Painting is a high-throughput phenotypic profiling assay that uses fluorescent cytochemistry to visualize a variety of organelles and high-content imaging to derive a large number of morphological features at the single-cell level. Most Cell Painting studies have used the U-2 OS cell line for chemical or functional genomics screening. The Cell Painting assay can be used with many other human-derived cell types, given that the assay is based on the use of fluoroprobes that label organelles that are present in most (if not all) human cells. Questions remain, however, regarding the optimization steps required and overall ease of deployment of the Cell Painting assay to novel cell types. Here, we used the Cell Painting assay to characterize the phenotypic effects of 14 phenotypic reference chemicals in concentration-response screening mode across six biologically diverse human-derived cell lines (U-2 OS, MCF7, HepG2, A549, HTB-9 and ARPE-19). All cell lines were labeled using the same cytochemistry protocol, and the same set of phenotypic features was calculated. We found it necessary to optimize image acquisition settings and cell segmentation parameters for each cell type, but did not adjust the cytochemistry protocol. For some reference chemicals, similar subsets of phenotypic features corresponding to a particular organelle were associated with the highest-effect magnitudes in each affected cell type. Overall, for certain chemicals, the Cell Painting assay yielded qualitatively similar biological activity profiles among a group of diverse, morphologically distinct human-derived cell lines without the requirement for cell type-specific optimization of cytochemistry protocols.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.