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Nat Commun. 2019 Apr 23;10(1):1903. doi: 10.1038/s41467-019-09670-4.

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.

Chen H1,2,3,4, Albergante L5,6,7, Hsu JY1,8, Lareau CA1,9, Lo Bosco G10,11, Guan J4, Zhou S12, Gorban AN13,14, Bauer DE9,15, Aryee MJ1,3,9, Langenau DM1,16, Zinovyev A5,6,7,14, Buenrostro JD9,17, Yuan GC18,19,20, Pinello L21,22.

Author information

1
Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.
2
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
3
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
4
Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China.
5
Institut Curie, PSL Research University, F-75005, Paris, France.
6
INSERM, U900, F-75005, Paris, France.
7
MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France.
8
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
9
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
10
Department of Mathematics and Computer Science, University of Palermo, 90123, Palermo, Italy.
11
Department of Sciences for technological innovation, Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy.
12
Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433, Shanghai, China.
13
Department of Mathematics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
14
Lobachevsky University, Nizhni Novgorod, 603022, Russia.
15
Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
16
Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
17
Harvard Society of Fellows, Harvard University, Cambridge, MA, 02138, USA.
18
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. gcyuan@jimmy.harvard.edu.
19
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. gcyuan@jimmy.harvard.edu.
20
Harvard Stem Cell Institute, Cambridge, MA, 02138, USA. gcyuan@jimmy.harvard.edu.
21
Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA. lpinello@mgh.harvard.edu.
22
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. lpinello@mgh.harvard.edu.

Abstract

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package.

PMID:
31015418
PMCID:
PMC6478907
DOI:
10.1038/s41467-019-09670-4
[Indexed for MEDLINE]
Free PMC Article

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