About 60% of lncRNA have a poly-A tail, as does mRNA. I wish to isolate only mRNA (by Qiagen kit). How do I get rid of the lncRNA or know that the transcripts I end up with are mRNA only?
Hi, if you perform mRNA isolation for RNA-Seq (using miRNeasy columns and performing DNAse treatment), after libprep and sequencing, majority of your reads would be mapped to the protein-coding genes with a minor part mapped to other types. To be on the safe side you may decide to use only "protein coding" genes in your later analysis.
Anyway, if you want to physically get rid of them, maybe CRISPR may be useful. We use it to get rid of the exceed of Mitochondrial-derived pieces in ATAC libraries (see http://p.labscout.cn/xiew/files/2016/11/CARM_20170404.pdf) . If there a DNA library for lncRNA available, I guess you might treat your library with it to get rid of the lncRNA-derived pieces.
Best,
Michail
I don't think there is an easy way to remove these. Why is it necessary to do so? Likely easier to filter them out in the analyses.
After the sequencing and demultiplexing of the samples you will have to map your reads to the reference transcriptome (for example, STAR). In the annotation for the genes in the count table you will also find the biotype. By filtering only for "protein coding" you will get rid of everything else.
Best,
Michail
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