Hi Dejan,
if I remember correctly (I haven't used the protocol since 2014), we didn't do anything special to freeze the pollen. You can, of course, quick freeze them (by using liquid nitrogen) and thawing them on ice is key. But pollen is really tough, therefore we didn't have problems. We anyways wanted to crush them after freezing and by doing FACS, we only collected the intact nuclei (which can be verified by microscopy after the sort).
The vegetative nuclei are more fragile than the sperm nuclei due to differences in DNA compaction. We also did ChIP with the sperm nuclei and had a hard time sonicating the nuclei to get the required 500bp fragments for sequencing. I wouldn't worry about the sperm nuclei. If you want to use the vegetative nuclei for a protocol that needs special handling, you will have to develop a freezing/thawing protocol on your own, but you can check the nuclei nicely under the microscope and distinguish sperm and vegetative nuclei by their shape and size.
I hope this helps.
Best,
Vera
2019-04-29 02:52:29