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Science. 2018 Jul 27;361(6400). pii: eaat5691. doi: 10.1126/science.aat5691. Epub 2018 Jun 21.

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

Author information

1
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
2
Neuroscience Program, Stanford University, CA 94305, USA.
3
Department of Psychiatry and Behavioral Sciences, Stanford University, CA 94305, USA.
4
Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
5
Department of Chemical Engineering, Stanford University, CA 94305, USA.
6
Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. deissero@stanford.edu alessio.bava@gmail.com gnolan@stanford.edu.
7
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. deissero@stanford.edu alessio.bava@gmail.com gnolan@stanford.edu.
8
Howard Hughes Medical Institute, Stanford University, CA 94305, USA.

Abstract

Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. We developed and applied a technology for 3D intact-tissue RNA sequencing, termed STARmap (spatially-resolved transcript amplicon readout mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy, and reproducibility. Moving to thick tissue blocks, we observed a molecularly defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells) and a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.

PMID:
29930089
DOI:
10.1126/science.aat5691
[Indexed for MEDLINE]

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