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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2023
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Materias: | |
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. |
format | Online Article Text |
id | pubmed-10635828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
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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