This article applies to CUT&RUN, meCUT&RUN and Multiomic CUT&RUN.
Important Notes
Trypan Blue is toxic to cells. After adding Trypan Blue dye to cells, move quickly to determine cell viability.
Materials needed
Reagent |
|---|
Trypan blue solution, 0.4% (e.g. Invitrogen T10282) |
Hemocytometer with brightfield/phase microscope or automated cell counter (e.g.) Countess automated cell counter) |
Protocol
Add 10 µL of 0.4% trypan blue to 10 µL washed cells/nuclei. Pipette to mix.
Transfer 10 µL of cell-trypan nlue mix to a counting slide.
View under brightfield/phase microscope or cell counter.
Assess cell/nuclei morphology and viability and troubleshoot as needed.
Viable cells are impermeable to trypan blue and will exclude the dye (trypan blue negative; Figure 1A).
Dead cells are permeable to trypan blue and will stain trypan blue positive (Figure 1A).
Isolated nuclei will stain trypan blue positive (Figure 1B).
.png)
Figure 1. (A) Washed K562 cells are mostly viable (bright white and round). A dead cell (blue, trypan positive) is circled in red. (B) Successful nuclei harvest shows trypan blue stained nuclei. An intact cell (bright white, trypan negative) is circled in red.