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Nat Methods DOI:10.1038/s41592-022-01667-0

High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations.

Publication TypeJournal Article
Year of Publication2022
AuthorsHaghighi, M, Caicedo, JC, Cimini, BA, Carpenter, AE, Singh, S
JournalNat Methods
Date Published2022 Nov 07

Cells can be perturbed by various chemical and genetic treatments and the impact on gene expression and morphology can be measured via transcriptomic profiling and image-based assays, respectively. The patterns observed in these high-dimensional profile data can power a dozen applications in drug discovery and basic biology research, but both types of profiles are rarely available for large-scale experiments. Here, we provide a collection of four datasets with both gene expression and morphological profile data useful for developing and testing multimodal methodologies. Roughly a thousand features are measured for each of the two data types, across more than 28,000 chemical and genetic perturbations. We define biological problems that use the shared and complementary information in these two data modalities, provide baseline analysis and evaluation metrics for multi-omic applications, and make the data resource publicly available ( ).


Alternate JournalNat Methods
PubMed ID36344834