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dc.contributor.authorHollfelder, Florian
dc.contributor.authorSalmen, F
dc.contributor.authorDe Jonghe, Joachim
dc.contributor.authorKaminski, T
dc.contributor.authorAlemany, A
dc.contributor.authorParada, G
dc.contributor.authorverity-Legg, Joe
dc.contributor.authorYanagida, A
dc.contributor.authorKohler, Timo
dc.contributor.authorBattich, N
dc.contributor.authorvan den Brekel, Floris
dc.contributor.authorEllermann, A
dc.contributor.authorMartinez Arias, A
dc.contributor.authorNichols, J
dc.contributor.authorHemberg, M
dc.contributor.authorvan Oudenaarden, A
dc.date.accessioned2022-03-28T23:30:39Z
dc.date.available2022-03-28T23:30:39Z
dc.identifier.issn1087-0156
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/335453
dc.description.abstractIn recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify the termini of polyadenylated transcripts capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts. Additionally, most workflows do not sequence the full transcript hindering the analysis of alternative splicing. We therefore developed VASAseq to detect the total transcriptome in single cells. VASA-seq is compatible with both platebased formats and droplet microfluidics. We applied VASA-seq to over 30,000 single cells in the developing mouse embryo during gastrulation and early organogenesis. The dynamics of the total single-cell transcriptome result in the discovery of novel cell type markers, many based on non-coding RNA, an in vivo cell cycle analysis and an improved RNA velocity characterization. Moreover, it provides the first comprehensive analysis of alternative splicing during mammalian development.
dc.description.sponsorshipBBSRC studentship to Joachim de Jonghe
dc.publisherNature Research
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleDroplet-based single-cell total RNA-seq reveals differential non-coding expression and splicing patterns during mouse development
dc.typeArticle
dc.publisher.departmentDepartment of Biochemistry
dc.date.updated2022-03-26T19:15:12Z
prism.publicationNameNature Biotechnology
dc.identifier.doi10.17863/CAM.82882
dcterms.dateAccepted2022-03-23
rioxxterms.versionAM
dc.contributor.orcidHollfelder, Florian [0000-0002-1367-6312]
rioxxterms.typeJournal Article/Review
cam.orpheus.counter24*
cam.depositDate2022-03-26
pubs.licence-identifierapollo-deposit-licence-2-1
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
rioxxterms.freetoread.startdate2025-03-28


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International