RT Journal Article
SR Electronic
T1 Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.04.06.535889
DO 10.1101/2023.04.06.535889
A1 McCormick, Caroline A.
A1 Akeson, Stuart
A1 Tavakoli, Sepideh
A1 Bloch, Dylan
A1 Klink, Isabel N.
A1 Jain, Miten
A1 Rouhanifard, Sara H.
YR 2024
UL http://biorxiv.org/content/early/2024/05/28/2023.04.06.535889.abstract
AB 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 in vitro transcription (IVT) of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analysis of human transcripts.Competing Interest StatementThe authors have declared no competing interest.DRSdirect RNA sequencingIVTin vitro transcriptionΨpseudouridinem6AN6-methyladenosineIinosinepoly-ApolyadenylatedgDNAgenomic DNApanIVTpooled aligned IVT readsBEDBrowser Extensible DataIGVintegrated genome viewingSNVsingle nucleotide variant