Integrative single-cell analysis

被引：917
作者：
Stuart, Tim [1 ]
Satija, Rahul [1 ,2 ]
机构：
[1] New York Genome Ctr, New York, NY 10013 USA
[2] NYU, Ctr Genom & Syst Biol, New York, NY 10003 USA
来源：
NATURE REVIEWS GENETICS | 2019年 / 20卷 / 05期
基金：
美国国家卫生研究院;
关键词：
MESSENGER-RNA-SEQ; GENE-EXPRESSION; CHROMATIN ACCESSIBILITY; DNA METHYLATION; SPATIAL RECONSTRUCTION; REGULATORY ELEMENTS; STEM-CELLS; GENOME; TRANSCRIPTOMICS; IDENTIFICATION;
D O I：
10.1038/s41576-019-0093-7
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic and lineage information in individual cells. This provides unique opportunities, alongside computational challenges, for integrative methods that can jointly learn across multiple types of data. Integrated analysis can discover relationships across cellular modalities, learn a holistic representation of the cell state, and enable the pooling of data sets produced across individuals and technologies. In this Review, we discuss the recent advances in the collection and integration of different data types at single-cell resolution with a focus on the integration of gene expression data with other types of single-cell measurement.
引用
收藏
页码：257 / 272
页数：16
相关论文
共 120 条
[91]   Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding [J].
Rosenberg, Alexander B. ;
Roco, Charles M. ;
Muscat, Richard A. ;
Kuchina, Anna ;
Sample, Paul ;
Yao, Zizhen ;
Graybuck, Lucas T. ;
Peeler, David J. ;
Mukherjee, Sumit ;
Chen, Wei ;
Pun, Suzie H. ;
Sellers, Drew L. ;
Tasic, Bosiljka ;
Seelig, Georg .
SCIENCE, 2018, 360 (6385) :176-+
[92]   Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state [J].
Rotem, Assaf ;
Ram, Oren ;
Shoresh, Noam ;
Sperling, Ralph A. ;
Goren, Alon ;
Weitz, David A. ;
Bernstein, Bradley E. .
NATURE BIOTECHNOLOGY, 2015, 33 (11) :1165-U91
[93]   Spatial reconstruction of single-cell gene expression data [J].
Satija, Rahul ;
Farrell, Jeffrey A. ;
Gennert, David ;
Schier, Alexander F. ;
Regev, Aviv .
NATURE BIOTECHNOLOGY, 2015, 33 (05) :495-U206
[94]   Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain [J].
Saunders, Arpiar ;
Macosko, Evan Z. ;
Wysoker, Alec ;
Goldman, Melissa ;
Krienen, Fenna M. ;
de Rivera, Heather ;
Bien, Elizabeth ;
Baum, Matthew ;
Bortolin, Laura ;
Wang, Shuyu ;
Goeva, Aleksandrina ;
Nemesh, James ;
Kamitaki, Nolan ;
Brumbaugh, Sara ;
Kulp, David ;
McCarroll, Steven A. .
CELL, 2018, 174 (04) :1015-+
[95]   Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding [J].
Schmidt, Stephanie Tzouanas ;
Zimmerman, Stephanie M. ;
Wang, Jianbin ;
Kini, Stuart K. ;
Quake, Stephen R. .
ACS SYNTHETIC BIOLOGY, 2017, 6 (06) :936-942
[96]   THE SEGMENTATION AND HOMEOTIC GENE NETWORK IN EARLY DROSOPHILA DEVELOPMENT [J].
SCOTT, MP ;
CARROLL, SB .
CELL, 1987, 51 (05) :689-698
[97]   Wishbone identifies bifurcating developmental trajectories from single-cell data [J].
Setty, Manu ;
Tadmor, Michelle D. ;
Reich-Zeliger, Shlomit ;
Ange, Omer ;
Salame, Tomer Meir ;
Kathail, Pooja ;
Choi, Kristy ;
Bendall, Sean ;
Friedman, Nir ;
Pe'er, Dana .
NATURE BIOTECHNOLOGY, 2016, 34 (06) :637-645
[98]   seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus [J].
Shah, Sheel ;
Lubeck, Eric ;
Zhou, Wen ;
Cai, Long .
NEURON, 2017, 94 (04) :752-+
[99]   In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus [J].
Shah, Sheel ;
Lubeck, Eric ;
Zhou, Wen ;
Cai, Long .
NEURON, 2016, 92 (02) :342-357
[100]   Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells [J].
Shalek, Alex K. ;
Satija, Rahul ;
Adiconis, Xian ;
Gertner, Rona S. ;
Gaublomme, Jellert T. ;
Raychowdhury, Raktima ;
Schwartz, Schraga ;
Yosef, Nir ;
Malboeuf, Christine ;
Lu, Diana ;
Trombetta, John J. ;
Gennert, Dave ;
Gnirke, Andreas ;
Goren, Alon ;
Hacohen, Nir ;
Levin, Joshua Z. ;
Park, Hongkun ;
Regev, Aviv .
NATURE, 2013, 498 (7453) :236-240
3456789101112