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-   -   miRNA and RNAseq - together or seperate? (http://seqanswers.com/forums/showthread.php?t=46280)

Elsie 08-31-2014 03:30 PM

miRNA and RNAseq - together or seperate?
 
Hi, I am interested in doing a miRNA NGS, specifically the TruSeq Small RNA Sample. I would also like to look more generally at RNAseq expression.
Should I do the TruSeq Small RNA sample kit *and* the TruSeq Stranded, so two different sets of data, or could I just do the TruSeq Small RNA Sample, will that also capture most of the other RNAseq info as well as the miRNAs, or does it really only focus on miRNAs and exclude everything else?

thanks.

nucacidhunter 09-01-2014 03:03 AM

Small RNA library preparation involves ligating adapters to termini of RNA and PCR after RT reaction. The reaction condition is optimised for amplification of small RNA species, so the larger RNA fractions will not amplify efficiently. In addition, there is a gel size selection step which cuts fragments generated from small RNA fraction for sequencing. RNAseq libraries are prepared by random priming of fragmented RNA, so the small RNA will not have much chance of primer binding and reverse transcription. If the aim is to study both small RNA and total RNA-rRNA or mRNA from the same sample, separate libraries have to be prepared for each.

Elsie 09-01-2014 01:35 PM

Thank you nucacidhunter, that is an extremely helpful answer and exactly what I was after!. I appreciate your time.

super0925 10-07-2014 04:04 AM

Hi All, I am doing RNA-Seq (reads mapped to human genome) and want to find significant Differential expressed genes, but I also find there is some reads counts mapped to miRNA, is it normal? Do I need to separate them to analysis it ? Or together analysis it? As nucacidhunter said, if I want to separate analysis , I need to re-prepare libraries (separate libraries)

Litania 12-13-2016 11:09 AM

What do you think about this article
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615683/
It claims that you can analyse both long and small RNA simultaneously


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