Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
Author:
Alon Shahar123ORCID, Goodwin Daniel R.12ORCID, Sinha Anubhav124ORCID, Wassie Asmamaw T.125, Chen Fei16, Daugharthy Evan R.78ORCID, Bando Yosuke19ORCID, Kajita Atsushi10, Xue Andrew G.1ORCID, Marrett Karl10, Prior Robert10ORCID, Cui Yi12ORCID, Payne Andrew C.16ORCID, Yao Chun-Chen16, Suk Ho-Jun124, Wang Ru12, Yu Chih-Chieh (Jay)125ORCID, Tillberg Paul1ORCID, Reginato Paul15678ORCID, Pak Nikita1211ORCID, Liu Songlei78ORCID, Punthambaker Sukanya78ORCID, Iyer Eswar P. R.8ORCID, Kohman Richie E.78ORCID, Miller Jeremy A.12ORCID, Lein Ed S.12ORCID, Lako Ana13ORCID, Cullen Nicole13, Rodig Scott13, Helvie Karla14, Abravanel Daniel L.61516ORCID, Wagle Nikhil14ORCID, Johnson Bruce E.14, Klughammer Johanna6ORCID, Slyper Michal6ORCID, Waldman Julia6ORCID, Jané-Valbuena Judit6ORCID, Rozenblatt-Rosen Orit6ORCID, Regev Aviv61718ORCID, Church George M.78ORCID, Marblestone Adam H.1, Boyden Edward S.1251718ORCID, Ali H. R., Al Sa’d M., Alon S., Aparicio S., Battistoni G., Balasubramanian S., Becker R., Bodenmiller B., Boyden E. S., Bressan D., Bruna A., Burger Marcel, Caldas C., Callari M., Cannell I. G., Casbolt H., Chornay N., Cui Y., Dariush A., Dinh K., Emenari A., Eyal-Lubling Y., Fan J., Fatemi A., Fisher E., González-Solares E. A., González-Fernández C., Goodwin D., Greenwood W., Grimaldi F., Hannon G. J., Harris O., Harris S., Jauset C., Joyce J. A., Karagiannis E. D., Kovačević T., Kuett L., Kunes R., Küpcü Yoldaş A., Lai D., Laks E., Lee H., Lee M., Lerda G., Li Y., McPherson A., Millar N., Mulvey C. M., Nugent F., O'Flanagan C. H., Paez-Ribes M., Pearsall I., Qosaj F., Roth A. J., Rueda O. M., Ruiz T., Sawicka K., Sepúlveda L. A., Shah S. P., Shea A., Sinha A., Smith A., Tavaré S., Tietscher S., Vázquez-García I., Vogl S. L., Walton N. A., Wassie A. T., Watson S. S., Weselak J., Wild S. A., Williams E., Windhager J., Whitmarsh T., Xia C., Zheng P., Zhuang X.,
Affiliation:
1. Department of Media Arts and Sciences, MIT, Cambridge, MA, USA. 2. McGovern Institute, MIT, Cambridge, MA, USA. 3. Faculty of Engineering, Gonda Brain Research Center and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel. 4. Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA. 5. Department of Biological Engineering, MIT, Cambridge, MA, USA. 6. Broad Institute of MIT and Harvard, Cambridge, MA, USA. 7. Department of Genetics, Harvard Medical School, Boston, MA, USA. 8. Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA. 9. Kioxia Corporation, Minato-ku, Tokyo, Japan. 10. Fixstars Solutions Inc, Irvine, CA, USA. 11. Department of Mechanical Engineering, MIT, Cambridge, MA, USA. 12. Allen Institute for Brain Science, Seattle, WA, USA. 13. Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA. 14. Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA. 15. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. 16. Department of Cell Biology, Harvard Medical School, Boston, MA, USA. 17. Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA. 18. Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Abstract
Identifying transcript location in cells
Identifying where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy has allowed for better visualization of small structures by expanding the tissues with a polymer- and hydrogel-based system. Alon
et al.
combined expansion microscopy with long-read in situ RNA sequencing, resulting in a more precise visualization of the location of specific transcripts. This method, termed “ExSeq” for expansion sequencing, was used to detect RNAs, both new transcripts and those previously demonstrated to localize to neuronal dendrites. Unlike other in situ sequencing methods, ExSeq does not target sets of genes. This technology thus unites spatial resolution, multiplexing, and an unbiased approach to reveal insights into RNA localization and its physiological roles in developing and active tissue.
Science
, this issue p.
eaax2656
Funder
National Science Foundation National Institutes of Health Howard Hughes Medical Institute Army Research Office Cancer Research UK IARPA Chan Zuckerberg Initiative
Publisher
American Association for the Advancement of Science (AAAS)
Subject
Multidisciplinary
Cited by
184 articles.
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