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

Xiao Wang | Zendy; William E. Allen | Zendy; Matthew A. Wright | Zendy; Emily L. Sylwestrak | Zendy; Nikolay Samusik | Zendy; Sam Vesuna | Zendy; Kathryn E. Evans | Zendy; Cindy Liu | Zendy; Charu Ramakrishnan | Zendy; Jia Liu | Zendy; Garry P. Nolan | Zendy; Felice-Alessio Bava | Zendy; Karl Deisseroth | Zendy

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

Author(s) -

Xiao Wang,

William E. Allen,

Matthew A. Wright,

Emily L. Sylwestrak,

Nikolay Samusik,

Sam Vesuna,

Kathryn E. Evans,

Cindy Liu,

Charu Ramakrishnan,

Jia Liu,

Garry P. Nolan,

Felice-Alessio Bava,

Karl Deisseroth

Publication year - 2018

Publication title -

science

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 12.556

H-Index - 1186

eISSN - 1095-9203

pISSN - 0036-8075

DOI - 10.1126/science.aat5691

Subject(s) - transcriptome , computational biology , biology , single cell sequencing , rna , in situ hybridization , dna sequencing , deep sequencing , illumina dye sequencing , in situ , gene , genetics , gene expression , genome , chemistry , exome sequencing , phenotype , organic chemistry

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.

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