OnRamp – 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.