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Wednesday, August 2 • 11:20 - 11:40
Direct RNA and cDNA sequencing of C. elegans transcripts

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Directly sequencing RNA, now possible through nanopore sequencing technologies, has the potential to improve upon cDNA sequencing efforts by streamlining library preparation, reducing batch effects, PCR bias, and template switching, and allowing for the direct detection of RNA modifications and polyadenylation status. We sought to benchmark direct RNA sequencing approaches against cDNA-based approaches by sequencing in parallel protein-coding RNA transcripts from wild-type C. elegans. We compared data quality, transcript abundance and full-length transcript recovery between the two sample preparation approaches. We tested multiple split read aligners (Exonerate, GMAP, LAST) to compare accuracy, identity and splice variant detection between them. We also assessed the extent to which direct RNA sequencing was able to detect known 3’ UTR isoforms and poly(A) tails, of biological interest due to their conserved and vital roles in post-transcriptional gene regulation, and validated splice variant detection using a known splicing mutant. Together, our results yardstick the sensitivity and accuracy of feature detection between direct RNA and cDNA sequencing.


Rachael Workman

Research specialist, Johns Hopkins University, Department of Biomedical Engineering

Wednesday August 2, 2017 11:20 - 11:40
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia