The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
Open accessAbstract
Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.
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Cites
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Cited by
Exploring tissue architecture using spatial transcriptomics
Rao, A., Barkley, D., França, G. S., & Yanai, I. (2021) · Nature · doi:10.1038/s41586-021-03634-9 · Cited by 1,700
Museum of spatial transcriptomics
Moses, L., & Pachter, L. (2022) · Nature Methods · doi:10.1038/s41592-022-01409-2 · Cited by 1,255
Museum of Spatial Transcriptomics
Moses, L., & Pachter, L. (2021) · doi:10.1101/2021.05.11.443152 · Cited by 1,255
Spatially resolved transcriptomes—next generation tools for tissue exploration
Asp, M., Bergenstråhle, J., & Lundeberg, J. (2020) · BioEssays · doi:10.1002/bies.201900221 · Cited by 666
Bressan, D., Battistoni, G., & Hannon, G. J. (2023) · Science · doi:10.1126/science.abq4964 · Cited by 594
Metadata
- Authors
- Gyllborg, D., Langseth, C. M., Qian, X., Choi, E., Salas, S. M., Hilscher, M. M., Lein, E. S., & Nilsson, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-09-29
- Volume
- 48
- Issue
- 19
- Pages
- e112-e112
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3090542854
- Cited by
- 303
- References
- 40
- FWCI
- 8.57
- Type
- journal article
- Language
- en
- Open access
- gold
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- Gyllborg, D., Langseth, C. M., Qian, X., Choi, E., Salas, S. M., Hilscher, M. M., Lein, E. S., & Nilsson, M. (2020). Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa792
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