Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
Top Cited Papers
- 29 January 2021
- journal article
- research article
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 371 (6528), 481-+
- https://doi.org/10.1126/science.aax2656
Abstract
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.Keywords
Funding Information
- National Science Foundation (DGE1144152)
- National Institutes of Health (1RM1HG008525)
- Howard Hughes Medical Institute (HHMI-Simons Faculty Scholars Program)
- Army Research Office (W911NF1510548)
- Cancer Research UK (C31893/A25050)
- IARPA (D16PC0008)
- Chan Zuckerberg Initiative (HCA Pilot Program)
This publication has 134 references indexed in Scilit:
- Patterns of mRNA and protein expression for 12 GABAA receptor subunits in the mouse brainNeuroscience, 2013
- The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution ImagingNeuron, 2012
- Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular SignaturesCell, 2012
- Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element RetrotransposonsNeuron, 2011
- Three groups of interneurons account for nearly 100% of neocortical GABAergic neuronsDevelopmental Neurobiology, 2010
- Aldehyde Dehydrogenase Activity of Breast Cancer Stem Cells Is Primarily Due To Isoform ALDH1A3 and Its Expression Is Predictive of MetastasisThe International Journal of Cell Cloning, 2010
- Cux1 and Cux2 Regulate Dendritic Branching, Spine Morphology, and Synapses of the Upper Layer Neurons of the CortexNeuron, 2010
- High-performance genetically targetable optical neural silencing by light-driven proton pumpsNature, 2010
- Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAsCurrent Opinion in Cell Biology, 2009
- Mechanisms and cellular roles of local protein synthesis in mammalian cellsCurrent Opinion in Cell Biology, 2008