I'm currently thinking about using flow cytometry to characterize and isolate individual cells from my sample that's encased in a hydrogel. This way, I can examine microbial growth rates among individual cells in the sample by using FISH. In theory, any sample containing a suspension of cells can be used for flow cytometry, but I also heard that only liquid samples can be used.
Now I'm aware that a hydrogel is liquid-like in that small molecules can diffuse in and out of the hydrogel, but it also has solid-like properties in that it doesn't exhibit nearly as much flow as a liquid sample. So in theory, could I use a hydrogel-encased sample for flow cytometry or not?
I don't think that would work without pre-processing your sample. My first suggestion is to digest the gel and release the cells into suspension for your flow cytometry. Depending on the gel type, enzymes or other chemical solutions can be used to do this.
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