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Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. Epub 2019 Sep 9.

High-definition spatial transcriptomics for in situ tissue profiling.

Author information

1
Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. vickovic@broadinstitute.org.
2
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. vickovic@broadinstitute.org.
3
Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
4
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
5
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
6
Center for Computational Biology, Flatiron Institute, New York, NY, USA.
7
Center for Data Science, New York University, New York, NY, USA.
8
Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
9
Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
10
Illumina, Inc., San Diego, CA, USA.
11
Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
12
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. joakim.lundeberg@scilifelab.se.
13
Department of Bioengineering, Stanford University, Stanford, CA, USA. joakim.lundeberg@scilifelab.se.
14
Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Abstract

Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.

PMID:
31501547
PMCID:
PMC6765407
[Available on 2020-03-09]
DOI:
10.1038/s41592-019-0548-y

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