Question: Is it possible to identify primary miRNA from scRNA seq?
gravatar for boting.m.ning
2.2 years ago by
boting.m.ning0 wrote:


This question might be quite stupid...

I have been working with miRNA sequencing and miRNA differential expression/correlation to mRNA targets related to diseases using small RNA seq. The results, as we all know, could be potentially confounded by cell type from the bulk RNA seq. Cell-type specific miRNA expression could greatly help me to interpret the results. There are some information for cell-type specific miRNA expression, but I couldn't find anything comprehensive.

While doing a single-cell miRNA seq ( such as Mime-seq by Alberti et al) might not be feasible for my lab, we do have a lot of single-cell RNA sequencing which utilizes 3' polyA tail. Also, even though the primary miRNAs are very rare and half extremely short half-life in the cells, they do have polyA tails, and could be theoretically be sequenced during the single-cell seq as well.

So I'm just wondering whether it is possible to computationally get the cell-type specific miRNA count from the 10x scRNA seq? Is there any strategy or tools that are suitable (such as modifying mirdeep2)? What type of gene reference data would be available?

Thank you all! Any suggestions are welcome!!

Best, BN

rna-seq • 1.4k views
ADD COMMENTlink written 2.2 years ago by boting.m.ning0

I would be very cautious with such an analysis

As far as I remember it is only the pri-miRNAs which have poly-a tails? Furthermore most RNAseq library preparation have a fragment size selection step. So theoretically I would not expect them to be there...?

Any analysis done would need to have a very good handle on the noise levels in the individual cells.

ADD REPLYlink written 2.2 years ago by kristoffer.vittingseerup3.5k
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