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https://hdl.handle.net/1822/56417
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Campo DC | Valor | Idioma |
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dc.contributor.author | Svensson, Valentine | por |
dc.contributor.author | Natarajan, Kedar Nath | por |
dc.contributor.author | Ly, Lam-Ha | por |
dc.contributor.author | Miragaia, Ricardo J. | por |
dc.contributor.author | Labalette, Charlotte | por |
dc.contributor.author | Macaulay, Iain C. | por |
dc.contributor.author | Cvejic, Ana | por |
dc.contributor.author | Teichmann, Sarah A. | por |
dc.date.accessioned | 2018-10-19T17:30:22Z | - |
dc.date.issued | 2017-03-06 | - |
dc.identifier.citation | Svensson, Valentine; Natarajan, Kedar Nath; Ly, Lam-Ha; Miragaia, Ricardo J.; Labalette, Charlotte; Macaulay, Iain C.; Cvejic, Ana; Teichmann, Sarah A., Power analysis of single-cell RNA-sequencing experiments. Nature Methods, 14(4), 381-387, 2017 | por |
dc.identifier.issn | 1548-7091 | por |
dc.identifier.uri | https://hdl.handle.net/1822/56417 | - |
dc.description | All data generated in this study have been deposited in the ArrayExpress database under accession codes E-MTAB-5480, E-MTAB-5481, E-MTAB-5482, E-MTAB-5483, E-MTAB-5484, E-MTAB-5485, and E-MTAB-5486. Summary tables are provided as supplementary files. | por |
dc.description.abstract | Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing. For our workflow, we developed a flexible tool for counting the number of unique molecular identifiers (https://github.com/vals/umis/). We compared 15 protocols computationally and 4 protocols experimentally for batch-matched cell populations, in addition to investigating the effects of spike-in molecular degradation. Our analysis provides an integrated framework for comparing scRNA-seq protocols. | por |
dc.description.sponsorship | We are grateful to O. Stegle and J.K. Kim for helpful discussions and comments on the manuscript. We thank M. Lynch for support with the C1 experiments, X. Chen for discussions on spike-ins, and M. Quail for help with 10× Chromium experiments. We extend our gratitude to S. Linnarsson and A. Zeisel for invaluable support in implementing STRT-seq in our laboratory and for help with sequencing the STRT library. We also thank D. Grün for sharing smFISH molecule counts. Finally we thank R. Kirchner for many improvements to the umis tool. This study was supported by Cancer Research UK grant C45041/A14953 to A.C. and C.L.; European Research Council project 677501–ZF_Blood to A.C.; a core support grant from the Wellcome Trust and MRC to the Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute; ERC grant ThSWITCH to S.A.T. (grant 260507); and a Lister Institute Research Prize to S.A.T. K.N.N. was supported by the Wellcome Trust Strategic Award ‘Single cell genomics of mouse gastrulation’. We thank P. Liu (Wellcome Trust Sanger Institute) for providing cells. | por |
dc.language.iso | eng | por |
dc.publisher | Springer Nature | por |
dc.relation | info:eu-repo/grantAgreement/EC/H2020/677501/EU | por |
dc.relation | info:eu-repo/grantAgreement/EC/FP7/260507/EU | por |
dc.rights | restrictedAccess | por |
dc.subject | Gene expression | por |
dc.subject | RNA sequencing | por |
dc.subject | Transcriptomics | por |
dc.title | Power analysis of single-cell RNA-sequencing experiments | por |
dc.type | article | - |
dc.peerreviewed | yes | por |
dc.relation.publisherversion | http://www.nature.com/nmeth/index.html | por |
dc.comments | CEB46719 | por |
oaire.citationStartPage | 381 | por |
oaire.citationEndPage | 387 | por |
oaire.citationIssue | 4 | por |
oaire.citationConferencePlace | United Kingdom | - |
oaire.citationVolume | 14 | por |
dc.date.updated | 2018-10-19T15:49:57Z | - |
dc.identifier.eissn | 1548-7105 | por |
dc.identifier.doi | 10.1038/nmeth.4220 | por |
dc.identifier.pmid | 28263961 | por |
dc.description.publicationversion | info:eu-repo/semantics/publishedVersion | por |
dc.subject.wos | Science & Technology | por |
sdum.journal | Nature Methods | por |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
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document_46719_1.pdf Acesso restrito! | 1,4 MB | Adobe PDF | Ver/Abrir |