Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Wednesday Speaker Abstracts

Metrology of Genome-Scale Measurements: Standards and Systematics to Get Comparability and Confidence

Marc Salit NIST, USA

No Abstract

A Reference Human Transcriptome Based on Native RNA Sequencing Miten Jain 1 ; Hugh E Olsen 1 ; Benedict Paten 1 ; Angela Brooks 1 ; Mark Akeson 1 ; 1 UC Santa Cruz, BME, Santa Cruz, California, United States

The Nanopore RNA consortium is an international consortium of Oxford Nanopore MinION and GridION users. In 2017, the consortium generated a dataset consisting of 13 million native RNA and 24 million cDNA strand reads based on poly-A RNA isolated from the human reference cell line GM12878. This dataset is publicly available on GitHub: https://github.com/nanopore-wgs- consortium/NA12878/blob/master/RNA.md. The median read identity for RNA strand reads was around 86%, and we observed aligned read lengths of up to 22 kb (116 exons). We also observed a strong correlation (R=0.875) between native RNA and cDNA datasets, and that 73% of annotated human reference transcripts were captured by the native RNA data. We anticipate this dataset will serve as a resource to the community for native RNA sequencing. We will present updates from the consortium work on analysis of these data that will include characterization of poly-A tail lengths using nanopore ionic current dwell time, assessment of full-length transcripts, detection of novel isoforms, and detection of base modifications using signal-level analysis.

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