A Review of the Application of Spatial Transcriptomics in Neuroscience

Zhang, Le; Xiong, Zhenqi; Xiao, Ming

doi:10.1007/s12539-024-00603-4

Interdiscip Sci Comput Life Sci

2024

DOI: 10.1007/s12539-024-00603-4

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A Review of the Application of Spatial Transcriptomics in Neuroscience

Le Zhang,

Zhenqi Xiong,

Ming Xiao

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Cited by 3 publications

References 150 publications

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Integration of Single-Cell and Spatial Transcriptomic Data Reveals Spatial Architecture and Potential Biomarkers in Alzheimer’s Disease

Fan,

2024

Mol Neurobiol

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Integration of Single-Cell and Spatial Transcriptomic Data Reveals Spatial Architecture and Potential Biomarkers in Alzheimer’s Disease

Fan,

2024

Mol Neurobiol

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Behavioral neuroscience: Flexible integration on the fly

Vogt

2024

Current Biology

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Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression during Tannin Biodegredation by Aspergillus tubingensis in Liquid and Solid Cultures

Zeng,

Song,

Tang

et al. 2024

IJMS

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Tannins, one of the most common anti-nutritional factors in feed, can be effectively degraded by various enzymes secreted by Aspergillus tubingensis (A. tubingensis). The cultivation method of fungi significantly impacts gene expression, which influences the production of enzymes and metabolites. In this study, we analyzed the tannin biodegredation efficiency and the transcriptomic responses of A. tubingensis in liquid and solid cultures with tannin added. The observed morphology of A. tubingensis resembled typical fungal hyphae of mycelium submerged and grown in liquid cultures, while mainly spore clusters were observed in solid cultures. Furthermore, the tannin biodegredation efficiency and protein secretion of A. tubingensis in liquid cultures were significantly higher than in solid cultures. Additionally, 54.6% of the 11,248 differentially expressed genes were upregulated in liquid cultures, including AtWU_03490 (encoding ABC multidrug transporter), AtWU_03807 (ribonuclease III), AtWU_10270 (peptidyl-tRNA hydrolase), and AtWU_00075 (arabinogalactan endo-1,4-beta-galactosidase). Functional and gene ontology enrichment analyses indicated upregulation in processes including oxidation reduction, drug metabolism, and monocarboxylic acid metabolism. Overall, this study provides insight into the transcriptomic response to tannin biodegradation by A. tubingensis in different cultures and reveals that liquid cultures induce greater transcriptomic variability compared to solid cultures.

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A Review of the Application of Spatial Transcriptomics in Neuroscience

Cited by 3 publications

References 150 publications

Integration of Single-Cell and Spatial Transcriptomic Data Reveals Spatial Architecture and Potential Biomarkers in Alzheimer’s Disease

Integration of Single-Cell and Spatial Transcriptomic Data Reveals Spatial Architecture and Potential Biomarkers in Alzheimer’s Disease

Behavioral neuroscience: Flexible integration on the fly

Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression during Tannin Biodegredation by Aspergillus tubingensis in Liquid and Solid Cultures

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