High-definition spatial transcriptomics for in situ tissue profiling

Sanja Vickovic; Gökcen Eraslan; Fredrik Salmén; Johanna Klughammer; Linnea Stenbeck; Denis Schapiro; Tarmo Äijö; Richard Bonneau; Ludvig Bergenstråhle; José Fernandéz Navarro; Joshua Gould; Gabriel K. Griffin; Åke Borg; Mostafa Ronaghi; Jonas Frisén; Joakim Lundeberg; Aviv Regev; Patrik L. Ståhl

doi:10.1038/s41592-019-0548-y

High-definition spatial transcriptomics for in situ tissue profiling

Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro, Joshua Gould, Gabriel K. Griffin, Åke Borg, Mostafa Ronaghi, Jonas Frisén, Joakim Lundeberg, Aviv Regev, Patrik L. Ståhl

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	987-990
Number of pages	4
Journal	Nature methods
Volume	16
Issue number	10
DOIs	https://doi.org/10.1038/s41592-019-0548-y
State	Published - Oct 1 2019

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., Gould, J., Griffin, G. K., Borg, Å., Ronaghi, M., Frisén, J., Lundeberg, J., Regev, A., & Ståhl, P. L. (2019). High-definition spatial transcriptomics for in situ tissue profiling. Nature methods, 16(10), 987-990. https://doi.org/10.1038/s41592-019-0548-y

Vickovic, S, Eraslan, G, Salmén, F, Klughammer, J, Stenbeck, L, Schapiro, D, Äijö, T, Bonneau, R, Bergenstråhle, L, Navarro, JF, Gould, J, Griffin, GK, Borg, Å, Ronaghi, M, Frisén, J, Lundeberg, J, Regev, A & Ståhl, PL 2019, 'High-definition spatial transcriptomics for in situ tissue profiling', Nature methods, vol. 16, no. 10, pp. 987-990. https://doi.org/10.1038/s41592-019-0548-y

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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.",

author = "Sanja Vickovic and G{\"o}kcen Eraslan and Fredrik Salm{\'e}n and Johanna Klughammer and Linnea Stenbeck and Denis Schapiro and Tarmo {\"A}ij{\"o} and Richard Bonneau and Ludvig Bergenstr{\aa}hle and Navarro, {Jos{\'e} Fernand{\'e}z} and Joshua Gould and Griffin, {Gabriel K.} and {\AA}ke Borg and Mostafa Ronaghi and Jonas Fris{\'e}n and Joakim Lundeberg and Aviv Regev and St{\aa}hl, {Patrik L.}",

note = "Funding Information: We thank the NGI Stockholm, SciLifeLab, Flatiron Institute and Simons Foundation for providing infrastructure support. We thank L. Gaffney, A. Hupalowska and J. Rood for help with manuscript preparation. Work was supported by the Knut and Alice Wallenberg Foundation, Swedish Foundation for Strategic Research, Swedish Cancer Society and the Swedish Research Council (to S.V., J.L. and P.L.S.), the EMBO long-term fellowship (no. ALTF 738-2017) to J.K., Early Postdoc Mobility fellowship (no. P2ZHP3_181475) to D.S., the NIH HuBMAP HIVE project and the Klarman Cell Observatory and HHMI (to A.R.). S.V is supported as a Wallenberg Fellow at the Broad Institute of MIT and Harvard. Publisher Copyright: {\textcopyright} 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.",

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doi = "10.1038/s41592-019-0548-y",

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AU - Vickovic, Sanja

AU - Eraslan, Gökcen

AU - Salmén, Fredrik

AU - Klughammer, Johanna

AU - Stenbeck, Linnea

AU - Schapiro, Denis

AU - Äijö, Tarmo

AU - Bonneau, Richard

AU - Bergenstråhle, Ludvig

AU - Navarro, José Fernandéz

AU - Gould, Joshua

AU - Griffin, Gabriel K.

AU - Borg, Åke

AU - Ronaghi, Mostafa

AU - Frisén, Jonas

AU - Lundeberg, Joakim

AU - Regev, Aviv

AU - Ståhl, Patrik L.

N1 - Funding Information: We thank the NGI Stockholm, SciLifeLab, Flatiron Institute and Simons Foundation for providing infrastructure support. We thank L. Gaffney, A. Hupalowska and J. Rood for help with manuscript preparation. Work was supported by the Knut and Alice Wallenberg Foundation, Swedish Foundation for Strategic Research, Swedish Cancer Society and the Swedish Research Council (to S.V., J.L. and P.L.S.), the EMBO long-term fellowship (no. ALTF 738-2017) to J.K., Early Postdoc Mobility fellowship (no. P2ZHP3_181475) to D.S., the NIH HuBMAP HIVE project and the Klarman Cell Observatory and HHMI (to A.R.). S.V is supported as a Wallenberg Fellow at the Broad Institute of MIT and Harvard. Publisher Copyright: © 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - 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.

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High-definition spatial transcriptomics for in situ tissue profiling

Abstract

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