Spatial Transcriptomics in Kidney Tissue.

Autor:	Raghubar AM; Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.; Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia.; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.; Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia.; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia., Crawford J; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia., Jones K; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia., Lam PY; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia., Andersen SB; Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia.; UQ Sequencing Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia., Matigian NA; QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia., Ng MSY; Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.; Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia.; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.; Nephrology Department, Princess Alexandra Hospital, Woolloongabba, QLD, Australia., Healy H; Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.; Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia.; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia., Kassianos AJ; Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.; Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia.; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia., Mallett AJ; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia. Andrew.Mallett@health.qld.gov.au.; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia. Andrew.Mallett@health.qld.gov.au.; College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia. Andrew.Mallett@health.qld.gov.au.; Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia. Andrew.Mallett@health.qld.gov.au.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2664, pp. 233-282.
DOI:	10.1007/978-1-0716-3179-9_17
Abstrakt:	Unlike bulk and single-cell/single-nuclei RNA sequencing methods, spatial transcriptome sequencing (ST-seq) resolves transcriptome expression within the spatial context of intact tissue. This is achieved by integrating histology with RNA sequencing. These methodologies are completed sequentially on the same tissue section placed on a glass slide with printed oligo-dT spots, termed ST-spots. Transcriptomes within the tissue section are captured by the underlying ST-spots and receive a spatial barcode in the process. The sequenced ST-spot transcriptomes are subsequently aligned with the hematoxylin and eosin (H&E) image, giving morphological context to the gene expression signatures within intact tissue. We have successfully employed ST-seq to characterize mouse and human kidney tissue. Here, we describe in detail the application of Visium Spatial Tissue Optimization (TO) and Visium Spatial Gene Expression (GEx) protocols for ST-seq in fresh frozen kidney tissue. (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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