Extended Data Fig. 3: Assessment of the effect of gene-treatment-related compounds on Cell Painting performance.
From: Optimizing the Cell Painting assay for image-based profiling
a, Addition of blasticidin to ORF plates or puromycin to CRISPR plates does not appear to improve cross-modailty matching across modalities versus unselected plates; compare the second and third columns to the first column in the top center, top-left and bottom-middle panels. b, Addition of selection compounds may have a deleterious effect on percent replicating versus unselected plates, although we cannot rule out that this is due to fewer replicates for the selected plates than the unselected ones. c, Addition of 4 µg/ml polybrene for 24 h may produce a phenotypic effect; polybrene addition displays decreased inter-treatment cross-plate percent replicating versus intra-treatment cross-plate-percent replicating (compare the center column to the outside columns), even though both sets of plates were stained and imaged as part of the same batch. d, Addition of polybrene to Target2-treated cells does not improve percent matching between Target2-treated plates and ORF-treated plates; note that the Target-ORF plates came from a previous batch and were not stained and imaged in parallel to the Target2 compound plates. For more information including the plate(s) represented by each data point, see the Source Data file for this figure; expanded experimental details for each plate may be found in Supplementary Data File 1.
