A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

Yue, Liangchen; Liu, Feng; Hu, Jiongsong; Peng, Yang; Wang, Yuxiang; Dong, Junguo; Shu, Wenjie; Huang, Xingxu; Wang, Shengqi

doi:10.1016/j.csbj.2023.01.016

Cited by 30 publications

(17 citation statements)

References 185 publications

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“…This suggests that the hypothalamus may not be well suited for bulk RNAseq studies due to the heterogeneity of the tissue. Future studies, particularly those using single cell methods (Kephart, 2023; Marquez-Galera et al, 2022; Yue et al, 2023) may further clarify the role that the hypothalamus plays in the overall response to dehydration.…”

Section: Discussionmentioning

confidence: 99%

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprivedPeromyscus eremicus

Blumstein,

MacManes

2024

Preprint

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The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduce food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintains tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex and successful response of regulatory processes.

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Section: Discussionmentioning

confidence: 99%

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprivedPeromyscus eremicus

Blumstein,

MacManes

2024

Preprint

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“…Furthermore, several preprocessing steps are commonly performed for both nonimaging and imaging‐based data, such as filtering genes and cells based on specific dataset thresholds (Dries, Chen, et al, 2021; Yue et al, 2023). Additionally, transformation of count data may be applied depending on downstream modeling assumptions (Liu, Li, & Zhang, 2022).…”

Section: Preprocessing Of Spatial Transcriptomics Datamentioning

confidence: 99%

Navigating the landscapes of spatial transcriptomics: How computational methods guide the way

Li,

Chen,

Yang

2024

WIREs RNA

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Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single‐cell, multi‐cellular, or sub‐cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi‐modal high‐throughput data source, which poses new challenges for the development of analytical methods for data‐mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever‐evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms.This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization

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“…67,68 Named "method of the year" in 2020 by Nature Methods, 72 spatially resolved transcriptomics can resolve gene expression across anatomical structures and regions by direct imaging or sequencing, at tens of micrometers down to the subcellular nanoscale resolution. 73,74 Currently, MGI offers the only sub-cellular resolution spatial transcriptomic profiler in the STOmics StereoSeq platform. 75 Boasting 500 nm sub-cellular resolution, 3D reconstruction capability, and capacity to analyze tissue sections up to 13 cm 2 , the STOmics platform can interrogate tumor cell heterogeneity and microenvironment, organism development, and whole organ profiling, among other applications.…”

Section: Single-cell Omics and Spatial Transcriptome Profilingmentioning

confidence: 99%

The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice

Kumar,

Cowley,

Davis

2024

Semin Thromb Hemost

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A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

Cited by 30 publications

References 185 publications

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprivedPeromyscus eremicus

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprivedPeromyscus eremicus

Navigating the landscapes of spatial transcriptomics: How computational methods guide the way

The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice

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