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

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-tis...

Full description

Saved in:
Bibliographic Details
Published in:Science (American Association for the Advancement of Science) Vol. 361; no. 6400
Main Authors: Wang, Xiao, Allen, William E, Wright, Matthew A, Sylwestrak, Emily L, Samusik, Nikolay, Vesuna, Sam, Evans, Kathryn, Liu, Cindy, Ramakrishnan, Charu, Liu, Jia, Nolan, Garry P, Bava, Felice-Alessio, Deisseroth, Karl
Format: Journal Article
Language:English
Published: United States 27.07.2018
Subjects:
Animals
Chromosome Mapping
Frontal Lobe - cytology
Frontal Lobe - metabolism
Imaging, Three-Dimensional
Male
Mice
Mice, Inbred C57BL
Molecular Imaging
Neurons - metabolism
Sequence Analysis, RNA - methods
Single-Cell Analysis - methods
Somatosensory Cortex - cytology
Somatosensory Cortex - metabolism
Transcription, Genetic
Transcriptome
Visual Cortex - cytology
Visual Cortex - metabolism
ISSN:1095-9203, 1095-9203
Online Access:Get more information
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ObjectType-Undefined-3
ISSN:1095-9203
1095-9203
DOI:10.1126/science.aat5691