Nanopore native RNA sequencing of a human poly(A) transcriptome.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
28
12
2018
accepted:
19
09
2019
pubmed:
20
11
2019
medline:
14
2
2020
entrez:
20
11
2019
Statut:
ppublish
Résumé
High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3' poly(A) tail length, base modifications and transcript haplotypes.
Identifiants
pubmed: 31740818
doi: 10.1038/s41592-019-0617-2
pii: 10.1038/s41592-019-0617-2
pmc: PMC7768885
mid: NIHMS1540455
doi:
Substances chimiques
Poly A
24937-83-5
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1297-1305Subventions
Organisme : NHLBI NIH HHS
ID : U01 HL137183
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM136577
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG008345
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010538
Pays : United States
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BB/N017099/1
Pays : International
Organisme : NHGRI NIH HHS
ID : R01 HG010053
Pays : United States
Organisme : Medical Research Council
ID : MR/M501621/1
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U54 HG007990
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Type : ErratumIn
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