Detection Of Linc Noncoding Rna

Question

[Honey]

I am trying to find how best I can design an experiment to detect linc noncoding RNA, Even though it is not related to downstream aspects per se, but before coming into real bioinformatics I am getting confused whether I am able to really detect and quantify such noncoding RNA or not. So far as I have read various papers have published using some kine of Ribo depletion and followed by RNA-seq which may obviously give me linc RNA. However following two posts (looks like users are quite expert in this filed), suggest otherwise

http://seqanswers.com/forums/showthread.php?t=27853&highlight=noncoding+rna

How To Design A Long Noncoding Rna Detection And Quantification Experiment

It appear that simple enrichment with ribo-depletion is not very relevant. Any suggestion what should be the best way to go - just ribodepleted or both polA vs Ribo-depleted libraries should be best to detect linc noncoding RNA.

Thanks Honey

[biorepine]

As you can see my answer in one of the links you provided, how one can extract lincRNAs from RNA-Seq. Regarding polyA vs ribo-depleted, can't you do both ?

Answer 1

[Honey]

I am open to do both However I am looking struggling with the fact how it can benefit me. Since till to date most of publications are suggesting just do Ribo-depleted and look for linc-noncoding RNA. If you want we can discuss it in more detail off the forum @ [e-mail]

Thanks