Reconstructing complex lineage trees from scRNA-seq data using MERLoT.
Algorithms
Animals
Cell Differentiation
/ genetics
Cell Lineage
/ genetics
Cluster Analysis
Gene Expression Profiling
/ methods
Hematopoietic Stem Cells
/ metabolism
Humans
Mice
Mouse Embryonic Stem Cells
/ metabolism
Sequence Analysis, RNA
/ methods
Single-Cell Analysis
/ methods
Software
Time Factors
Transcriptome
/ genetics
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
26 09 2019
26 09 2019
Historique:
accepted:
01
08
2019
revised:
22
07
2019
received:
18
12
2018
pubmed:
21
8
2019
medline:
21
12
2019
entrez:
21
8
2019
Statut:
ppublish
Résumé
Advances in single-cell transcriptomics techniques are revolutionizing studies of cellular differentiation and heterogeneity. It has become possible to track the trajectory of thousands of genes across the cellular lineage trees that represent the temporal emergence of cell types during dynamic processes. However, reconstruction of cellular lineage trees with more than a few cell fates has proved challenging. We present MERLoT (https://github.com/soedinglab/merlot), a flexible and user-friendly tool to reconstruct complex lineage trees from single-cell transcriptomics data. It can impute temporal gene expression profiles along the reconstructed tree. We show MERLoT's capabilities on various real cases and hundreds of simulated datasets.
Identifiants
pubmed: 31428793
pii: 5552070
doi: 10.1093/nar/gkz706
pmc: PMC6755101
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
8961-8974Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Elife. 2017 Dec 05;6:
pubmed: 29206104
Genome Biol. 2017 Sep 12;18(1):174
pubmed: 28899397
Cell. 2015 May 21;161(5):1202-1214
pubmed: 26000488
Nat Commun. 2019 Apr 23;10(1):1903
pubmed: 31015418
Genome Biol. 2016 May 23;17(1):106
pubmed: 27215581
Nat Biotechnol. 2019 May;37(5):547-554
pubmed: 30936559
Bioinformatics. 2019 Sep 15;35(18):3517-3519
pubmed: 30715210
Nature. 2016 Jun 08;534(7607):391-5
pubmed: 27281220
Science. 2017 Aug 18;357(6352):661-667
pubmed: 28818938
Nucleic Acids Res. 2016 Jul 27;44(13):e117
pubmed: 27179027
Nat Biotechnol. 2014 Apr;32(4):381-386
pubmed: 24658644
Cell. 2015 May 21;161(5):1187-1201
pubmed: 26000487
FEBS Lett. 2017 Aug;591(15):2213-2225
pubmed: 28524227
BMC Genomics. 2018 Jun 19;19(1):477
pubmed: 29914354
Bioinformatics. 2016 Apr 15;32(8):1241-3
pubmed: 26668002
Nat Biotechnol. 2016 Nov 8;34(11):1145-1160
pubmed: 27824854
Genome Res. 2015 Oct;25(10):1491-8
pubmed: 26430159
Science. 2018 Oct 26;362(6413):
pubmed: 30262634
Nat Methods. 2017 Oct;14(10):979-982
pubmed: 28825705
Mol Biol Evol. 1987 Jul;4(4):406-25
pubmed: 3447015
Nat Cell Biol. 2017 Apr;19(4):271-281
pubmed: 28319093
Dev Cell. 2010 Apr 20;18(4):675-85
pubmed: 20412781
Proc Natl Acad Sci U S A. 2005 May 24;102(21):7426-31
pubmed: 15899970
Cell. 2015 Dec 17;163(7):1663-77
pubmed: 26627738