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Old 05-02-2014, 09:18 AM   #1
Erlkoenig
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Location: USA

Join Date: May 2014
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Default Small RNA library: 30nt peak?

I performed an RNA-seq experiment and observed an unusual size distribution of small RNAs (image attached). I was wondering if anyone has seen this before.

I used Ambion's mirVana small RNA kit to extract and enrich for the sRNA fraction (<200nt). Used the Ion Total RNA-seq kit v2 to create libraries, and the Ion Proton platform for sequencing. In addition to the 21-24 nt peak corresponding to miRNA and siRNA, my libraries include a ton of ~30 nt reads after mapping to my genome.

I tried Rfam and some tRNA databases, but didn't have any luck annotating them. When I BLASTed the most abundant 30nt reads at NCBI, it returned protein-coding genes from various organisms. My RNA prep was clean, with no significant degradation. The peak is broad but well-defined, dropping off around 36nt.

Could these mystery reads be some kind of noncoding RNA that I simply haven't heard of? Are you familiar with this type of length distribution?
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Old 05-09-2014, 01:07 PM   #2
cascoamarillo
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.........piRNAs?
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