TY - JOUR
T1 - Expansion sequencing
T2 - Spatially precise in situ transcriptomics in intact biological systems
AU - IMAXT Consortium
AU - Alon, Shahar
AU - Goodwin, Daniel R.
AU - Sinha, Anubhav
AU - Wassie, Asmamaw T.
AU - Chen, Fei
AU - Daugharthy, Evan R.
AU - Bando, Yosuke
AU - Kajita, Atsushi
AU - Xue, Andrew G.
AU - Marrett, Karl
AU - Prior, Robert
AU - Cui, Yi
AU - Payne, Andrew C.
AU - Yao, Chun Chen
AU - Suk, Ho Jun
AU - Wang, Ru
AU - Yu, Chih Chieh
AU - Tillberg, Paul
AU - Reginato, Paul
AU - Pak, Nikita
AU - Liu, Songlei
AU - Punthambaker, Sukanya
AU - Iyer, Eswar P.R.
AU - Kohman, Richie E.
AU - Miller, Jeremy A.
AU - Lein, Ed S.
AU - Lako, Ana
AU - Cullen, Nicole
AU - Rodig, Scott
AU - Helvie, Karla
AU - Abravanel, Daniel L.
AU - Wagle, Nikhil
AU - Johnson, Bruce E.
AU - Klughammer, Johanna
AU - Slyper, Michal
AU - Waldman, Julia
AU - Jané-Valbuena, Judit
AU - Rozenblatt-Rosen, Orit
AU - Regev, Aviv
AU - Church, George M.
AU - Marblestone, Adam H.
AU - Boyden, Edward S.
N1 - Publisher Copyright:
© 2021 American Association for the Advancement of Science. All rights reserved.
PY - 2021/1/29
Y1 - 2021/1/29
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85100446979&partnerID=8YFLogxK
U2 - 10.1126/science.aax2656
DO - 10.1126/science.aax2656
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C2 - 33509999
AN - SCOPUS:85100446979
SN - 0036-8075
VL - 371
JO - Science
JF - Science
IS - 6528
M1 - aax2656
ER -