Open-source, high-throughput targeted <i>in situ</i> transcriptomics for developmental and tissue biology
Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
Authors
- Mats F. Nilsson (ORCID: https://orcid.org/0000-0001-9985-0387)
- Eneritz Rueda-Alaña (ORCID: https://orcid.org/0000-0003-3045-4970)
- Sergio Marco Salas (ORCID: https://orcid.org/0000-0002-4636-0322)
- Andreas Metousis (ORCID: https://orcid.org/0000-0002-1043-6591)
- Hower Lee (ORCID: https://orcid.org/0000-0002-8781-3623)
- Emma K. Lundberg (ORCID: https://orcid.org/0000-0001-7034-0850)
- Marco Grillo (ORCID: https://orcid.org/0000-0003-2155-0645)
- Fernando García‐Moreno (ORCID: https://orcid.org/0000-0001-9048-4237)
- Christoffer Mattsson Langseth (ORCID: https://orcid.org/0000-0003-2230-8594)
- Sanem Sarıyar (ORCID: https://orcid.org/0000-0003-0735-5595)
- Christina Bekiari (ORCID: https://orcid.org/0009-0006-7735-9830)
Institutions
- Ikerbasque (ES)
- Stockholm University (SE)
- University of the Basque Country (ES)
- Science for Life Laboratory (SE)
- Achucarro Basque Center for Neuroscience (ES)
- KTH Royal Institute of Technology (SE)
- Stanford University (US)
Publication Details
- Journal
- Development
- Published
- 2024-08-05
- DOI
- https://doi.org/10.1242/dev.202448
- Citations
- 4
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.94
Funders
- Silicon Valley Community Foundation
- Familjen Erling-Perssons Stiftelse
- Chan Zuckerberg Initiative
- Cancerfonden
- Eusko Jaurlaritza
- Ikerbasque, Basque Foundation for Science
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- Ministerio de Ciencia e Innovación
- Stockholms Universitet