High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atla...

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Autores principales: Vahid, Milad R., Brown, Erin L., Steen, Chloé B., Zhang, Wubing, Jeon, Hyun Soo, Kang, Minji, Gentles, Andrew J., Newman, Aaron M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2023
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10635828/
https://www.ncbi.nlm.nih.gov/pubmed/36879008
http://dx.doi.org/10.1038/s41587-023-01697-9
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author Vahid, Milad R.
Brown, Erin L.
Steen, Chloé B.
Zhang, Wubing
Jeon, Hyun Soo
Kang, Minji
Gentles, Andrew J.
Newman, Aaron M.
author_facet Vahid, Milad R.
Brown, Erin L.
Steen, Chloé B.
Zhang, Wubing
Jeon, Hyun Soo
Kang, Minji
Gentles, Andrew J.
Newman, Aaron M.
author_sort Vahid, Milad R.
collection PubMed
description Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.
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spelling pubmed-106358282023-11-15 High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE Vahid, Milad R. Brown, Erin L. Steen, Chloé B. Zhang, Wubing Jeon, Hyun Soo Kang, Minji Gentles, Andrew J. Newman, Aaron M. Nat Biotechnol Brief Communication Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution. Nature Publishing Group US 2023-03-06 2023 /pmc/articles/PMC10635828/ /pubmed/36879008 http://dx.doi.org/10.1038/s41587-023-01697-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Communication
Vahid, Milad R.
Brown, Erin L.
Steen, Chloé B.
Zhang, Wubing
Jeon, Hyun Soo
Kang, Minji
Gentles, Andrew J.
Newman, Aaron M.
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title_full High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title_fullStr High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title_full_unstemmed High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title_short High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
title_sort high-resolution alignment of single-cell and spatial transcriptomes with cytospace
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10635828/
https://www.ncbi.nlm.nih.gov/pubmed/36879008
http://dx.doi.org/10.1038/s41587-023-01697-9
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