2021/08/28 by Caitlin E. Mills, Kartik Subramanian, Marc Hafner +9 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Cell Image Analysis Techniques #Single-cell and spatial transcriptomics #Advanced Fluorescence Microscopy Techniques
paper · pdf · doi:10.1101/2021.08.27.457854
openalex publication_date 2021/08/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
ABSTRACT High-throughput measurement of cells perturbed using libraries of small molecules, gene knockouts, or different microenvironmental factors is a key step in functional genomics and pre-clinical drug discovery. However, it remains difficult to perform accurate single-cell assays in 384-well plates, limiting many studies to well-average measurements (e.g. CellTiter-Glo®). Here we describe a public domain “Dye Drop” method that uses sequential density displacement and microscopy to perform multi-step assays on living cells. We use Dye Drop cell viability and DNA replication assays followed by immunofluorescence imaging to collect single-cell dose-response data for 67 investigational and clinical-grade small molecules in 58 breast cancer cell lines. By separating the cytostatic and cytotoxic effects of drugs computationally, we uncover unexpected relationships between the two. Dye Drop is rapid, reproducible, customizable, and compatible with manual or automated laboratory equipment. Dye Drop improves the tradeoff between data content and cost, enabling the collection of information-rich perturbagen-response datasets.