It turns out that it doesn't really matter when I freeze the sample, I can get high-quality RNA either way:
All 6 of my samples came out with really high RIN numbers. Talking with J~, it seems that the best way to go is to freeze the sample after the phenol-chloroform separation stage. At this point the RNA is pretty clean, certainly more so than in the RNAsolv buffer and I haven't used any of the columns or anything. Further, we're unclear of how the phenol-based RNAsolv buffer holds up for long-term freezing (this was only frozen for 2 days), whereas the top separated layer should remain stable frozen indefinitely.
Now, on to my samples!
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