High-definition spatial transcriptomics for in situ tissue profiling
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 expe...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2020
|
| Online Access: | https://hdl.handle.net/1721.1/126032 |
| _version_ | 1826191801452593152 |
|---|---|
| author | Vickovic, Sanja Eraslan, Gökcen Salmén, Fredrik Klughammer, Johanna Stenbeck, Linnea Schapiro, Denis Äijö, Tarmo Bonneau, Richard Bergenstråhle, Ludvig Navarro, José Fernandéz Gould, Joshua Griffin, Gabriel K. Borg, Åke Ronaghi, Mostafa Frisén, Jonas Lundeberg, Joakim Regev, Aviv Ståhl, Patrik L. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Vickovic, Sanja Eraslan, Gökcen Salmén, Fredrik Klughammer, Johanna Stenbeck, Linnea Schapiro, Denis Äijö, Tarmo Bonneau, Richard Bergenstråhle, Ludvig Navarro, José Fernandéz Gould, Joshua Griffin, Gabriel K. Borg, Åke Ronaghi, Mostafa Frisén, Jonas Lundeberg, Joakim Regev, Aviv Ståhl, Patrik L. |
| author_sort | Vickovic, Sanja |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T09:01:31Z |
| format | Article |
| id | mit-1721.1/126032 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:01:31Z |
| publishDate | 2020 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1260322022-09-26T09:55:31Z High-definition spatial transcriptomics for in situ tissue profiling Vickovic, Sanja Eraslan, Gökcen Salmén, Fredrik Klughammer, Johanna Stenbeck, Linnea Schapiro, Denis Äijö, Tarmo Bonneau, Richard Bergenstråhle, Ludvig Navarro, José Fernandéz Gould, Joshua Griffin, Gabriel K. Borg, Åke Ronaghi, Mostafa Frisén, Jonas Lundeberg, Joakim Regev, Aviv Ståhl, Patrik L. Massachusetts Institute of Technology. Department of Biology Koch Institute for Integrative Cancer Research at MIT 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. 2020-06-30T21:35:49Z 2020-06-30T21:35:49Z 2019-09 2019-03 2020-03-17T18:00:43Z Article http://purl.org/eprint/type/JournalArticle 1548-7091 1548-7105 https://hdl.handle.net/1721.1/126032 Vickovic, Sanja et al. "High-definition spatial transcriptomics for in situ tissue profiling." Nature Methods 16, 10 (September 2019): 987–990 © 2019 The Author(s) en http://dx.doi.org/10.1038/s41592-019-0548-y Nature Methods Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Springer Science and Business Media LLC PMC |
| spellingShingle | Vickovic, Sanja Eraslan, Gökcen Salmén, Fredrik Klughammer, Johanna Stenbeck, Linnea Schapiro, Denis Äijö, Tarmo Bonneau, Richard Bergenstråhle, Ludvig Navarro, José Fernandéz Gould, Joshua Griffin, Gabriel K. Borg, Åke Ronaghi, Mostafa Frisén, Jonas Lundeberg, Joakim Regev, Aviv Ståhl, Patrik L. High-definition spatial transcriptomics for in situ tissue profiling |
| title | High-definition spatial transcriptomics for in situ tissue profiling |
| title_full | High-definition spatial transcriptomics for in situ tissue profiling |
| title_fullStr | High-definition spatial transcriptomics for in situ tissue profiling |
| title_full_unstemmed | High-definition spatial transcriptomics for in situ tissue profiling |
| title_short | High-definition spatial transcriptomics for in situ tissue profiling |
| title_sort | high definition spatial transcriptomics for in situ tissue profiling |
| url | https://hdl.handle.net/1721.1/126032 |
| work_keys_str_mv | AT vickovicsanja highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT eraslangokcen highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT salmenfredrik highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT klughammerjohanna highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT stenbecklinnea highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT schapirodenis highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT aijotarmo highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT bonneaurichard highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT bergenstrahleludvig highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT navarrojosefernandez highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT gouldjoshua highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT griffingabrielk highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT borgake highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT ronaghimostafa highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT frisenjonas highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT lundebergjoakim highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT regevaviv highdefinitionspatialtranscriptomicsforinsitutissueprofiling AT stahlpatrikl highdefinitionspatialtranscriptomicsforinsitutissueprofiling |