Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes

Spatially resolved transcriptomics (SrT) allow researchers to explore organ/tissue architecture from the angle of the gene programs involved in their molecular complexity. Here, we describe the use of MULTILAYER to reveal molecular tissue substructures from the analysis of localized transcriptomes (...

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Autores principales: Moehlin, Julien, Koshy, Aysis, Stüder, François, Mendoza-Parra, Marco Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8450297/
https://www.ncbi.nlm.nih.gov/pubmed/34585159
http://dx.doi.org/10.1016/j.xpro.2021.100823
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author Moehlin, Julien
Koshy, Aysis
Stüder, François
Mendoza-Parra, Marco Antonio
author_facet Moehlin, Julien
Koshy, Aysis
Stüder, François
Mendoza-Parra, Marco Antonio
author_sort Moehlin, Julien
collection PubMed
description Spatially resolved transcriptomics (SrT) allow researchers to explore organ/tissue architecture from the angle of the gene programs involved in their molecular complexity. Here, we describe the use of MULTILAYER to reveal molecular tissue substructures from the analysis of localized transcriptomes (defined as gexels). MULTILAYER can process low- and high-resolution SrT data but also perform comparative analyses within multiple SrT readouts. For complete details on the use and execution of this protocol, please refer to Moehlin et al., 2021.
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spelling pubmed-84502972021-09-27 Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes Moehlin, Julien Koshy, Aysis Stüder, François Mendoza-Parra, Marco Antonio STAR Protoc Protocol Spatially resolved transcriptomics (SrT) allow researchers to explore organ/tissue architecture from the angle of the gene programs involved in their molecular complexity. Here, we describe the use of MULTILAYER to reveal molecular tissue substructures from the analysis of localized transcriptomes (defined as gexels). MULTILAYER can process low- and high-resolution SrT data but also perform comparative analyses within multiple SrT readouts. For complete details on the use and execution of this protocol, please refer to Moehlin et al., 2021. Elsevier 2021-09-14 /pmc/articles/PMC8450297/ /pubmed/34585159 http://dx.doi.org/10.1016/j.xpro.2021.100823 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Moehlin, Julien
Koshy, Aysis
Stüder, François
Mendoza-Parra, Marco Antonio
Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title_full Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title_fullStr Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title_full_unstemmed Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title_short Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes
title_sort protocol for using multilayer to reveal molecular tissue substructures from digitized spatial transcriptomes
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8450297/
https://www.ncbi.nlm.nih.gov/pubmed/34585159
http://dx.doi.org/10.1016/j.xpro.2021.100823
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