Core lab webinar series: A new 'gold standard' solution for complete plasmid sequencing

Event overview

During our second installment of the series, the speakers shared how nanopore sequencing can be used to validate plasmids. Members of the Oxford Nanopore team took us through the protocol for plasmid sequencing using Oxford Nanopore Rapid Barcoding Kits and how to approach analysing the data created. When then heard from our guest speaker, Mel Englund, Postdoctoral Researcher in the Boyle Lab at the University of Michigan. Mel discussed using nanopore sequencing for rapid, multiplexed validation of plasmids.

On-Ramp: a tool for rapid, multiplexed validation of plasmids using nanopore sequencing

Abstract

Sequence validation is an essential step in any plasmid cloning workflow. However, existing validation tools suffer from either a lack of scalability (e.g., Sanger sequencing) or a lack of affordability and accessibility (e.g., next-generation sequencing). OnRamp (Oxford Nanopore-based Rapid Analysis of Multiplexed Plasmids) leverages nanopore sequencing technology to bridge the gap between these existing validation methods. It addresses the need for a rapid, straightforward, and cost-effective protocol for multiplexed validation of full plasmid sequences. OnRamp also addresses the need for accessibility across labs with different levels of bioinformatic expertise, as the OnRamp webapp (onramp.boylelab.org) can be used to analyze data and generate results in an easily interpretable format.

During the webinar Mel:

• Described the OnRamp wet-lab protocols and data analysis pipeline
• Showed how the OnRamp webapp can be used for easy analysis and interpretation
• Shared results which demonstrated the power of nanopore-based plasmid sequencing to capture cryptic errors in plasmids

Meet the speaker

Mel Englund is a Postdoctoral Researcher in the Boyle Lab at the University of Michigan. Mel’s research focuses on the development and design of plasmid-based reporter assays for the characterization of cis-regulatory elements in the human genome, with an emphasis on their use in studying silencers and enhancer blockers. Her work aims to expand our understanding of how interactions between different classes of non-coding sequences in both plasmid and genomic contexts can impact gene expression.

A new and improved 'gold standard' in plasmid sequencing services for core labs

Abstract

Aaron started by introducing why the field is moving towards routine whole plasmid verification, and how the Oxford Nanopore workflow enables core labs to provide their customers with a new and improved plasmid sequencing solution. Jemma then walked attendees through the protocol for plasmid sequencing using Oxford Nanopore Rapid Barcoding Kits. Followed by Stephen, who introduced EPI2ME bioinformatics and cover democratising data analyses for non-bioinformaticians.

Aaron Pomerantz is the Segment Marketing Manager at Oxford Nanopore, where he covers synthetic biology, microbiology and infectious disease. He received his PhD from UC Berkeley in the Department of Integrative Biology, employing genomics, genome editing, and bioimaging techniques in non-model organisms, as well as in-field nanopore sequencing in the Amazon rainforest. In his role as Segment Marketing Manager, he drives development of new areas in the research life sciences market.

Jemma Jordan is a Director within the Product Management team at Oxford Nanopore and is responsible for their range of library preparation kits. She has a PhD in Biochemistry and over a decade of laboratory experience developing and optimising assays and workflows.

Stephen Rudd is a Director at Oxford Nanopore where he is responsible for the bioinformatic products and imagines user journeys that begin with a collection of FASTQ files. He has two decades of experience in genome bioinformatics support and works with the Customer Workflows team towards demystifying bioinformatics. Through our EPI2ME Labs environment, we hope to support laboratory scientists with simplified solutions to complex computational tasks.