Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH

被引：1077

作者：

Eng, Chee-Huat Linus ^{[1
]}

Lawson, Michael ^{[2
]}

Zhu, Qian ^{[3
,4
]}

Dries, Ruben ^{[3
,4
]}

Koulena, Noushin ^{[2
]}

Takei, Yodai ^{[2
]}

Yun, Jina ^{[2
]}

Cronin, Christopher ^{[2
]}

Karp, Christoph ^{[2
]}

Yuan, Guo-Cheng ^{[3
,4
]}

Cai, Long ^{[2
]}

机构：

[1] CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA

[2] CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA

[3] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[4] Harvard TH Chan Sch Publ Hlth, Boston, MA USA

来源：

NATURE | 2019年 / 568卷 / 7751期

关键词：

STATISTICAL SIGNIFICANCE; SINGLE; REVEALS; CELLS;

D O I：

10.1038/s41586-019-1049-y

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：

07 ; 0710 ; 09 ;

摘要：

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells(1-5). Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells-with high accuracy and sub-diffraction-limit resolution-in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand-receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ.

引用

页码：235 / +

页数：22

共 41 条

[21] Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions [J].

Mili, Stavroula ;

Moissoglu, Konstadinos ;

Macara, Ian G. .

NATURE, 2008, 453 (7191) :115-+

[22] High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing [J].

Moffitt, Jeffrey R. ;

Hao, Junjie ;

Bambah-Mukku, Dhananjay ;

Lu, Tian ;

Dulac, Catherine ;

Zhuang, Xiaowei .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (50) :14456-14461

[23]

Parthasarathy R, 2012, NAT METHODS, V9, P724, DOI [10.1038/NMETH.2071, 10.1038/nmeth.2071]

[24] Imaging individual mRNA molecules using multiple singly labeled probes [J].

Raj, Arjun ;

van den Bogaard, Patrick ;

Rifkin, Scott A. ;

van Oudenaarden, Alexander ;

Tyagi, Sanjay .

NATURE METHODS, 2008, 5 (10) :877-879

[25] A draft network of ligand-receptor-mediated multicellular signalling in human [J].

Ramilowski, Jordan A. ;

Goldberg, Tatyana ;

Harshbarger, Jayson ;

Kloppman, Edda ;

Lizio, Marina ;

Satagopam, Venkata P. ;

Itoh, Masayoshi ;

Kawaji, Hideya ;

Carninci, Piero ;

Rost, Burkhard ;

Forrest, Alistair R. R. .

NATURE COMMUNICATIONS, 2015, 6

[26] Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) [J].

Rust, Michael J. ;

Bates, Mark ;

Zhuang, Xiaowei .

NATURE METHODS, 2006, 3 (10) :793-795

[27] 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-+

[28] Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function [J].

Shah, Prajay T. ;

Stratton, Jo A. ;

Stykel, Morgan Gail ;

Abbasi, Sepideh ;

Sharma, Sandeep ;

Mayr, Kyle A. ;

Koblinger, Kathrin ;

Whelan, Patrick J. ;

Biernaskie, Jeff .

CELL, 2018, 173 (04) :1045-+

[29] Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH [J].

Shah, Sheel ;

Takei, Yodai ;

Zhou, Wen ;

Lubeck, Eric ;

Yun, Jina ;

Eng, Chee-Huat Linus ;

Koulena, Noushin ;

Cronin, Christopher ;

Karp, Christoph ;

Liaw, Eric J. ;

Amin, Mina ;

Cai, Long .

CELL, 2018, 174 (02) :363-+

[30] 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

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