[Histonet] E18.5 embryo processing issues

[M.O.]

Hello Histonetters!

We have started to work on paraffin processing on E18.5 to P1/2 mouse
embryos and would love to have insights into the issues we are having. We
believe we are running into some processing issues as some of the organs
such as the liver and heart are very crunchy, and they are not staying
where they should be located. We have been poking some holes with needles
in the tissue, but it seems not helping much. Would cutting into the skin
be a better option?

The protocol we have at the moment is:
Tissue fixing in 4%PFA at 4 degree C overnight
PBS washes 30mins 4 times at 4 degree C
30% Ethanol 2 hours
50% Ethanol 2 hours
70% Ethanol 2 hours
And then subject to paraffin embedding machine for a long processing
protocol that takes 2 days.

I've seen protocols that use NBF at higher temperatures for fixation,
however we are trying to do some spatial assays and RNA degradation is a
concern if using a higher temperature.

For our other tissues of bone and cartilage, we've used zinc buffered
formalin at RT without issues downstream for spatial/FISH.

Thank you again for any tips!
-Merissa