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

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...

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Detalles Bibliográficos
Autores principales: McCormick, Caroline A., Akeson, Stuart, Tavakoli, Sepideh, Bloch, Dylan, Klink, Isabel N., Jain, Miten, Rouhanifard, Sara H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104151/
https://www.ncbi.nlm.nih.gov/pubmed/37066160
http://dx.doi.org/10.1101/2023.04.06.535889
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author McCormick, Caroline A.
Akeson, Stuart
Tavakoli, Sepideh
Bloch, Dylan
Klink, Isabel N.
Jain, Miten
Rouhanifard, Sara H.
author_facet McCormick, Caroline A.
Akeson, Stuart
Tavakoli, Sepideh
Bloch, Dylan
Klink, Isabel N.
Jain, Miten
Rouhanifard, Sara H.
author_sort McCormick, Caroline A.
collection PubMed
description 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.
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spelling pubmed-101041512023-04-15 Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis McCormick, Caroline A. Akeson, Stuart Tavakoli, Sepideh Bloch, Dylan Klink, Isabel N. Jain, Miten Rouhanifard, Sara H. bioRxiv Article 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. Cold Spring Harbor Laboratory 2023-04-06 /pmc/articles/PMC10104151/ /pubmed/37066160 http://dx.doi.org/10.1101/2023.04.06.535889 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
McCormick, Caroline A.
Akeson, Stuart
Tavakoli, Sepideh
Bloch, Dylan
Klink, Isabel N.
Jain, Miten
Rouhanifard, Sara H.
Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title_full Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title_fullStr Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title_full_unstemmed Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title_short Multicellular, IVT-derived, unmodified human transcriptome for nanopore direct RNA analysis
title_sort multicellular, ivt-derived, unmodified human transcriptome for nanopore direct rna analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104151/
https://www.ncbi.nlm.nih.gov/pubmed/37066160
http://dx.doi.org/10.1101/2023.04.06.535889
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