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

被引：181

作者：

Chen, Huidong ^{[1
,2
,3
,4
,5
,6
]}

Albergante, Luca ^{[7
,8
,9
]}

Hsu, Jonathan Y. ^{[1
,2
,3
,10
]}

Lareau, Caleb A. ^{[1
,2
,3
,11
]}

Lo Bosco, Giosue ^{[12
,13
]}

Guan, Jihong ^{[6
]}

Zhou, Shuigeng ^{[14
,15
]}

Gorban, Alexander N. ^{[16
,17
]}

Bauer, Daniel E. ^{[11
,18
]}

Aryee, Martin J. ^{[1
,2
,3
,5
,11
]}

Langenau, David M. ^{[1
,2
,3
,19
]}

Zinovyev, Andrei ^{[7
,8
,9
,17
]}

Buenrostro, Jason D. ^{[11
,20
]}

Yuan, Guo-Cheng ^{[4
,5
,19
]}

Pinello, Luca ^{[1
,2
,3
,11
]}

机构：

[1] Massachusetts Gen Hosp, Res Inst, Mol Pathol Unit, Boston, MA 02114 USA

[2] Massachusetts Gen Hosp, Res Inst, Canc Ctr, Boston, MA 02114 USA

[3] Harvard Med Sch, Boston, MA 02114 USA

[4] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02215 USA

[5] Harvard TH Chan Sch Publ Hlth, Dept Biostat, Boston, MA 02215 USA

[6] Tongji Univ, Dept Comp Sci & Technol, Shanghai 201804, Peoples R China

[7] PSL Res Univ, Inst Curie, F-75005 Paris, France

[8] INSERM, U900, F-75005 Paris, France

[9] PSL Res Univ, CBIO Ctr Computat Biol, MINES ParisTech, F-75006 Paris, France

[10] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[11] MIT & Harvard, Brd Inst, Cambridge, MA 02142 USA

[12] Univ Palermo, Dept Math & Comp Sci, I-90123 Palermo, Italy

[13] Euro Mediterranean Inst Sci & Technol, Dept Sci Technol Innovat, I-90139 Palermo, Italy

[14] Fudan Univ, Shanghai Key Lab Intelligent Informat Proc, Shanghai 200433, Peoples R China

[15] Fudan Univ, Sch Comp Sci, Shanghai 200433, Peoples R China

[16] Univ Leicester, Dept Math, Univ Rd, Leicester LE1 7RH, Leics, England

[17] Lobachevsky Univ, Nizhnii Novgorod 603022, Russia

[18] Harvard Med Sch, Oncol Boston Childrens Hosp, Dana Farber Canc Inst, Dept Pediat,Div Hematol, Boston, MA 02215 USA

[19] Harvard Stem Cell Inst, Cambridge, MA 02138 USA

[20] Harvard Univ, Harvard Soc Fellows, Cambridge, MA 02138 USA

来源：

NATURE COMMUNICATIONS | 2019年 / 10卷 / 1期

基金：

中国国家自然科学基金;

关键词：

EMBRYONIC STEM-CELLS; MESSENGER-RNA-SEQ; CHROMATIN ACCESSIBILITY; DIFFERENTIATION; HETEROGENEITY; DYNAMICS; BIOLOGY;

D O I：

10.1038/s41467-019-09670-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

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.

引用

页数：14

共 58 条

[1]

Albergante L, 2018, ROBUST SCALABLE LEAR

[2]

[Anonymous], 2008, Principal manifolds for data visualization and dimension reduction, DOI DOI 10.1007/978-3-540-73750-6_5

[3]

[Anonymous], 2016, NUCL ACIDS RES, DOI DOI 10.1093/NAR/GKW430

[4]

[Anonymous], 2009, HDB RES MACHINE LEAR

[5]