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Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis.

ABSTRACT: Nanopore direct RNA sequencing (DRS) enables measurements of native RNA modifications. Modification-free transcripts are an important control for DRS. Additionally, it is advantageous to have canonical transcripts from multiple cell lines to better account for human transcriptome variation. Here we generated and analyzed Nanopore DRS datasets for five human cell lines using in vitro transcribed (IVT) RNA. We compared performance statistics amongst biological replicates. We also documented nucleotide and ionic current level variation across cell lines. These data will serve as a resource to the community for RNA modification analysis.

SUBMITTER: McCormick CA

PROVIDER: S-EPMC10104151 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis.

McCormick Caroline A CA Akeson Stuart S Tavakoli Sepideh S Bloch Dylan D Klink Isabel N IN Jain Miten M Rouhanifard Sara H SH

bioRxiv : the preprint server for biology 20240528

Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analysis. We produced DRS datasets using modification-free transcripts from <i>in vitro</i> transcription (IVT) of cDN ...[more]

PMID: 37066160

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