Table 1:
Details of dyes, stained cellular sub-compartments, and channels imaged in the Cell Painting assay
| Channel name | |||
|---|---|---|---|
| Dye | Organelle or cellular component | CellProfiler | ImageXpress |
| Hoechst 33 342 | Nucleus | DNA | w1 |
| Concanavalin A/Alexa Fluor 488 conjugate | Endoplasmic reticulum | ER | w2 |
| SYTO 14 green fluorescent nucleic acid stain | Nucleoli, cytoplasmic RNA | RNA | w3 |
| Phalloidin/Alexa Fluor 594 conjugate, wheat germ agglutinin (WGA)/Alexa Fluor 594 conjugate | F-actin cytoskeleton, Golgi, plasma membrane | AGP | w4 |
| MitoTracker Deep Red | Mitochondria | Mito | w5 |
The CellProfiler channel name refers to the name given by the software to each channel; this nomenclature also applies to the naming of the extracted morphological features. The ImageXpress channel name refers to the text in the raw image file name identifying the acquired wavelength. Please note that this protocol was later updated to use Phalloidin/Alexa Fluor 568 and WGA/Alexa Fluor 555, as described in [9].