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. 2023:2664:233-282.
doi: 10.1007/978-1-0716-3179-9_17.

Spatial Transcriptomics in Kidney Tissue

Arti M Raghubar  1   2   3   4   5 , Joanna Crawford  5 , Kahli Jones  5   6 , Pui Y Lam  5 , Stacey B Andersen  7   8 , Nicholas A Matigian  9 , Monica S Y Ng  1   2   5   10 , Helen Healy  1   2   3 , Andrew J Kassianos  1   2   3 , Andrew J Mallett  11   12   13   14
Affiliations

Spatial Transcriptomics in Kidney Tissue

Arti M Raghubar et al. Methods Mol Biol. 2023.

Abstract

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.

Keywords: Kidney; Spatial transcriptomics; Visium Spatial Gene Expression; Visium Spatial Tissue Optimization.

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