Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

• DOI: 10.1126/science.aax2656
• Publication Date: 2021-01-28T20:10:24Z
• Authors: Shahar Alon; Daniel R. Goodwin; Anubhav Sinha; Asmamaw T. Wassie; Fei Chen; Evan R. Daugharthy; Yosuke Bando; Atsushi Kajita; Andrew G. Xue; Karl Marrett; Robert Prior; Yi Cui; Andrew C. Payne; Chun-Chen Yao; Ho-Jun Suk; Ru Wang; Chih-Chieh (Jay) Yu; Paul Tillberg; Paul Reginato; Nikita Pak; Songlei Liu; Sukanya Punthambaker; Eswar P. R. Iyer; Richie E. Kohman; Jeremy A. Miller; Ed S. Lein; Ana Lako; Nicole Cullen; Scott Rodig; Karla Helvie; Daniel L. Abravanel; Nikhil Wagle; Bruce E. Johnson; Johanna Klughammer; Michal Slyper; Julia Waldman; Judit Jané-Valbuena; Orit Rozenblatt-R...; Aviv Regev; ; George M. Church; Adam H. Marblestone; Edward S. Boyden; H. R. Ali; M. Al Sa’d; S. Alon; S. Aparicio; G. Battistoni; S. Balasubramanian; R. Becker; B. Bodenmiller; E. S. Boyden; D. Bressan; A. Bruna; Marcel Burger; C. Caldas; M. Callari; I. G. Cannell; H. Casbolt; N. Chornay; Y. Cui; A. Dariush; K. Dinh; A. Emenari; Y. Eyal-Lubling; J. Fan; A. Fatemi; E. Fisher; E. A. González-So...; C. González-Ferná...; D. Goodwin; W. Greenwood; F. Grimaldi; G. J. Hannon; O. Harris; S. Harris; C. Jauset; J. A. Joyce; E. D. Karagiannis; T. Kovačević; L. Kuett; R. Kunes; A. Küpcü Yoldaş; D. Lai; E. Laks; H. Lee; M. Lee; G. Lerda; Y. Li; A. McPherson; N. Millar; C. M. Mulvey; F. Nugent; C. H. O'Flanagan; M. Paez-Ribes; I. Pearsall; F. Qosaj; A. J. Roth; O. M. Rueda; T. Ruiz; K. Sawicka; L. A. Sepúlveda; S. P. Shah; A. Shea; A. Sinha; A. Smith; S. Tavaré; S. Tietscher; I. Vázquez-García; S. L. Vogl; N. A. Walton; A. T. Wassie; S. S. Watson; J. Weselak; S. A. Wild; E. Williams; J. Windhager; T. Whitmarsh; C. Xia; P. Zheng; X. Zhuang
• Keywords: 0301 basic medicine; 0303 health sciences; Sequence Analysis, RNA; Dendritic Spines; Gene Expression Profiling; Breast Neoplasms; Molecular Imaging; 3. Good health; Mice; 03 medical and health sciences; Animals; Humans; Female; Single-Cell Analysis; Visual Cortex

Identifying transcript location in cells where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy allowed for better visualization of small structures expanding the tissues with polymer- hydrogel-based system. Alon et al. combined expansion long-read situ RNA sequencing, resulting more precise transcripts. This method, termed “ExSeq” was used to detect RNAs, both new transcripts those previously demonstrated localize neuronal dendrites. Unlike other sequencing methods, ExSeq does not target sets genes. thus unites spatial resolution, multiplexing, an unbiased approach reveal insights into localization its physiological roles developing active tissue. Science , this issue p. eaax2656