in situ hybr. of lncRNA - stains both sense and antisense

[JonB]

This might not be the correct place for this post, but please point me in the right direction of you know of other forums.

I have stained three different lncRNAs (probes are between 700-1000nts) with DIG ISH. And all the probes are stained in both directions. I do not know how to explain this. I know that many lncRNAs are expressed antisense to protein coding genes, but not these ones. The lncRNAs are also, to some extent, self complementary which could explain this.

Anyone have any suggestions to how I can address this further? Or have good explations for this?

Thanks,

Jon