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Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue

Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including Slide-seqV2, have achieved spatial transcriptomic data collection at a near-single cell resolution. To-date, a repertoire of computational tools ha...

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Autores principales: Noel, Teia, Wang, Qingbo S., Greka, Anna, Marshall, Jamie L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8770822/
https://www.ncbi.nlm.nih.gov/pubmed/35069263
http://dx.doi.org/10.3389/fphys.2021.809346
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author Noel, Teia
Wang, Qingbo S.
Greka, Anna
Marshall, Jamie L.
author_facet Noel, Teia
Wang, Qingbo S.
Greka, Anna
Marshall, Jamie L.
author_sort Noel, Teia
collection PubMed
description Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including Slide-seqV2, have achieved spatial transcriptomic data collection at a near-single cell resolution. To-date, a repertoire of computational tools has been developed to discern cell type classes given the transcriptomic profiles of tissue coordinates. Upon applying these tools, we can explore the spatial patterns of distinct cell types and characterize how genes are spatially expressed within different cell type contexts. The kidney is one organ whose function relies upon spatially defined structures consisting of distinct cellular makeup. Thus, the application of Slide-seqV2 to kidney tissue has enabled us to elucidate spatially characteristic cellular and genetic profiles at a scale that remains largely unexplored. Here, we review spatial transcriptomic technologies, as well as computational approaches for cell type mapping and spatial cell type and transcriptomic characterizations. We take kidney tissue as an example to demonstrate how the technologies are applied, while considering the nuances of this architecturally complex tissue.
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spelling pubmed-87708222022-01-21 Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue Noel, Teia Wang, Qingbo S. Greka, Anna Marshall, Jamie L. Front Physiol Physiology Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including Slide-seqV2, have achieved spatial transcriptomic data collection at a near-single cell resolution. To-date, a repertoire of computational tools has been developed to discern cell type classes given the transcriptomic profiles of tissue coordinates. Upon applying these tools, we can explore the spatial patterns of distinct cell types and characterize how genes are spatially expressed within different cell type contexts. The kidney is one organ whose function relies upon spatially defined structures consisting of distinct cellular makeup. Thus, the application of Slide-seqV2 to kidney tissue has enabled us to elucidate spatially characteristic cellular and genetic profiles at a scale that remains largely unexplored. Here, we review spatial transcriptomic technologies, as well as computational approaches for cell type mapping and spatial cell type and transcriptomic characterizations. We take kidney tissue as an example to demonstrate how the technologies are applied, while considering the nuances of this architecturally complex tissue. Frontiers Media S.A. 2022-01-06 /pmc/articles/PMC8770822/ /pubmed/35069263 http://dx.doi.org/10.3389/fphys.2021.809346 Text en Copyright © 2022 Noel, Wang, Greka and Marshall. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Physiology
Noel, Teia
Wang, Qingbo S.
Greka, Anna
Marshall, Jamie L.
Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title_full Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title_fullStr Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title_full_unstemmed Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title_short Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue
title_sort principles of spatial transcriptomics analysis: a practical walk-through in kidney tissue
topic Physiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8770822/
https://www.ncbi.nlm.nih.gov/pubmed/35069263
http://dx.doi.org/10.3389/fphys.2021.809346
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