PT  - JOURNAL ARTICLE
AU  - Shahar Alon
AU  - Daniel R Goodwin
AU  - Anubhav Sinha
AU  - Asmamaw T Wassie
AU  - Fei Chen
AU  - Evan R Daugharthy
AU  - Yosuke Bando
AU  - Atsushi Kajita
AU  - Andrew G Xue
AU  - Karl Marrett
AU  - Robert Prior
AU  - Yi Cui
AU  - Andrew C Payne
AU  - Chun-Chen Yao
AU  - Ho-Jun Suk
AU  - Ru Wang
AU  - Chih-Chieh (Jay) Yu
AU  - Paul Tillberg
AU  - Paul Reginato
AU  - Nikita Pak
AU  - Songlei Liu
AU  - Sukanya Punthambaker
AU  - Eswar P. R. Iyer
AU  - Richie E Kohman
AU  - Jeremy A Miller
AU  - Ed S Lein
AU  - Ana Lako
AU  - Nicole Cullen
AU  - Scott Rodig
AU  - Karla Helvie
AU  - Daniel L Abravanel
AU  - Nikhil Wagle
AU  - Bruce E Johnson
AU  - Johanna Klughammer
AU  - Michal Slyper
AU  - Julia Waldman
AU  - Judit Jané-Valbuena
AU  - Orit Rozenblatt-Rosen
AU  - Aviv Regev
AU  - IMAXT Consortium
AU  - George M Church
AU  - Adam H Marblestone
AU  - Edward S Boyden
TI  - Expansion Sequencing: Spatially Precise <em>In Situ</em> Transcriptomics in Intact Biological Systems
AID  - 10.1101/2020.05.13.094268
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.13.094268
4099  - http://biorxiv.org/content/early/2020/05/15/2020.05.13.094268.short
4100  - http://biorxiv.org/content/early/2020/05/15/2020.05.13.094268.full
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 mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across 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.One Sentence Summary In situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.Competing Interest StatementThe authors have declared no competing interest.