ABSTRACT
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 Statement
The authors have declared no competing interest.
Footnotes
RESEARCH AREA: Genetics and Genomics
CLASSIFICATIONS: Transcriptomics; Bioinformatics
DATA DESCRIPTION
This version of the manuscript has been revised to reflect the peer-reviewed version
ABBREVIATIONS
- DRS
- direct RNA sequencing
- IVT
- in vitro transcription
- Ψ
- pseudouridine
- m6A
- N6-methyladenosine
- I
- inosine
- poly-A
- polyadenylated
- gDNA
- genomic DNA
- panIVT
- pooled aligned IVT reads
- BED
- Browser Extensible Data
- IGV
- integrated genome viewing
- SNV
- single nucleotide variant
