In my DAPI stainings, I noticed that DAPI disparately labels retinal cells. Sometimes, ganglion cells are brightly labelled, other times they are faintly labelled. Usually, amacrine and bipolar cell stainings are brightly labelled in weakly ganglion cell --labelled retinas, with little or no horizontal cell labelling. I was also wondering whether DAPI preferentially labels OFF bipolar cells compared to ON bipolar cells. Does it have to do with the concentration or incubation time? I guess DAPI staining is rather random.
I don't know about your specific cells but I also find that DAPI doesn't always stain all cells equally, and I tried asking people about it but they don't seem to know the reason.
In addition to concentration and time, DAPI staining fluctuates depending on chromatin condensation, histone acetylation and spurious factors, such as tissue fixation. When conditions are well controlled, DAPI staining can help pinpointing certain cell types, detection of cell death, and cell cycle phases, but there are much better markers for identification of various retinal cell types.
@ Yulia Panina
Same story here. I even observe that DAPI labelling is sometimes disparate across different retinas.
@ Rafael Linden
Thank you for the useful comments. Indeed, there are better markers for retinal cells post-fixation. However, in my case, I need to label retinal cells before fixation. The goal is to identify certain retinal cells in order to inject them with dyes or tracers. For this specific purpose, I guess the most commonly used markers are Acridine Orange (labels ganglion cells) and DAPI/Hoechst (labels all retinal cells). Each of the three markers stains DNA. It is however interesting that labelling of retinal cells by DAPI is rather irregular or disparate compared to that by Acridine Orange.
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