Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.
IF: 63.714
Cited by: 149


Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.


Spatial Transcriptomics

MeSH terms

Breast Neoplasms
Dendritic Spines
Gene Expression Profiling
Molecular Imaging
Sequence Analysis, RNA
Single-Cell Analysis
Visual Cortex


Alon, Shahar
Goodwin, Daniel R
Sinha, Anubhav
Wassie, Asmamaw T
Chen, Fei
Daugharthy, Evan R
Bando, Yosuke
Kajita, Atsushi
Xue, Andrew G
Marrett, Karl
Prior, Robert
Cui, Yi
Payne, Andrew C
Yao, Chun-Chen
Suk, Ho-Jun
Wang, Ru
Yu, Chih-Chieh Jay
Tillberg, Paul
Reginato, Paul
Pak, Nikita
Liu, Songlei
Punthambaker, Sukanya
Iyer, Eswar P R
Kohman, Richie E
Miller, Jeremy A
Lein, Ed S
Lako, Ana
Cullen, Nicole
Rodig, Scott
Helvie, Karla
Abravanel, Daniel L
Wagle, Nikhil
Johnson, Bruce E
Klughammer, Johanna
Slyper, Michal
Waldman, Julia
Jané-Valbuena, Judit
Rozenblatt-Rosen, Orit
Regev, Aviv
Church, George M
Marblestone, Adam H
Boyden, Edward S

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