REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
QIAGEN RNeasy Mini Kit (250)	Qiagen	74106
Dynabeads™ mRNA Purification Kit	ThermoFisher Scientific	61006
Direct RNA sequencing kit	Oxford Nanopore Technologies	SQK-RNA002
Flow Cell Priming Kit	Oxford Nanopore Technologies	EXP-FLP002
PromethION Flow Cell	Oxford Nanopore Technologies	FLO-PRO002
Ethanol absolute for analysis	Merck	1009831000
Nuclease-free water	Qiagen	129114
SuperScript III Reverse Transcriptase	ThermoFisher Scientific	18080044
10 mM dNTP solution	NEB	N0447
NEBNext® Quick Ligation Reaction Buffer	NEB	B6058
T4 DNA Ligase 2M U/ml	NEB	M0202
Agencourt RNAClean XP beads	Beckman Coulter	A63987
Qubit RNA HS Assay Kit	ThermoFisher Scientific	Q32852
Qubit dsDNA HS Assay Kit	ThermoFisher Scientific	Q32851
KAPA Stranded RNA-Seq Library Preparation Kit	Roche	KR0934
SeqCap Adapter Kit A	Roche	07141530001
Deposited data
Raw data	This paper	GEO:
Mouse reference genome (mm10)	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/
Mouse gene annotation (M25)	Gencode	https://www.gencodegenes.org/mouse/release_M25.html
Raw sequence reads	SRA	PRJNA779821
Experimental models: Organisms/strains
Mus musculus C57BL/6JArc	Australian Resource Centre	Cat No.: 000664
Software and algorithms
R		Version 3.6.3
R Studio	https://www.rstudio.com/products/rstudio	Version 1.2.5033
Minimap2	https://github.com/lh3/minimap2	Version 2.17-r941
Nanocompore	https://github.com/tleonardi/nanocompore	v1.0.3
Xpore	https://github.com/GoekeLab/xpore	Version 2.0
F5c	https://github.com/hasindu2008/f5c	Version 0.8
Scripts	Zenodo	https://doi.org/10.5281/zenodo.6782309