Cell Painting Dataset of EUbOPEN compounds

This parquet file is a dataset of cell painting profiles generated using a technique of morphological profiling known as the Cell Painting Assay (CPA). The CPA aims at deeply characterizing modulator from their ‘fingerprint’ in human cells as seen in microscopic images.

Cells subjected to treatments are fixed, stained and imaged. These images are analysed and more than 7500 features are extracted using a cell profiler pipeline. Single cell level profiles are aggregated into well-level profiles which can be used to compare and contrast chemical treatments.

Morphological profiling using cell painting begins with the culture of bone sarcoma U2OS cells in control and perturbation conditions for 24 to 48 hours. These cells are then subjected to 4% PFA fixation and staining with 6 inorganic dyes (Hoechst 33342 Nuclear Stain, Concanavalin A 488, Nucleic Acid Stain, WGA 555, Phalloidin 568, Mitotracker Mitochondrial stain 641) in order to mark 8 cellular components (nucleus, endoplasmic reticulum, mitochondria, actin, Golgi, plasma membrane, nucleolus and RNA). Images at 20x magnification are then captured using a high content microscope Yokogawa Cell Voyager CV8000. These images go through a rigorous quality control process  are then passed through the profiling pipeline using the open-source software Cell Profiler. Thousands of features are extracted from each image and value of each feature is computed so as to detect even the slightest phenotypic variation occurring in cells in an extremely sensitive manner.

This dataset consists of profiles of 595 compounds from the EUbOPEN consortium (cell painting first batch) in 106 plates in the 384 well format. DMSO and positive controls are present in columns 1,2, 23 and 24. There are 39206 rows, each row corresponding to one well, and 7721 columns. The treatments have been done in a range of 8 doses and the highest dose treatment has been done at 2 time points.