Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization

There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example...

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Detalles Bibliográficos
Autores principales: Sona, Surbhi, Bradley, Matthew, Ting, Angela H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9871342/
https://www.ncbi.nlm.nih.gov/pubmed/36853708
http://dx.doi.org/10.1016/j.xpro.2023.102047
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author Sona, Surbhi
Bradley, Matthew
Ting, Angela H.
author_facet Sona, Surbhi
Bradley, Matthew
Ting, Angela H.
author_sort Sona, Surbhi
collection PubMed
description There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results. For complete details on the use and execution of this protocol, please refer to Fink et al. (2022).(1)
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spelling pubmed-98713422023-01-25 Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization Sona, Surbhi Bradley, Matthew Ting, Angela H. STAR Protoc Protocol There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results. For complete details on the use and execution of this protocol, please refer to Fink et al. (2022).(1) Elsevier 2023-01-19 /pmc/articles/PMC9871342/ /pubmed/36853708 http://dx.doi.org/10.1016/j.xpro.2023.102047 Text en © 2023 The Authors 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
Sona, Surbhi
Bradley, Matthew
Ting, Angela H.
Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title_full Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title_fullStr Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title_full_unstemmed Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title_short Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization
title_sort protocols for single-cell rna-seq and spatial gene expression integration and interactive visualization
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9871342/
https://www.ncbi.nlm.nih.gov/pubmed/36853708
http://dx.doi.org/10.1016/j.xpro.2023.102047
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