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Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]

ABSTRACT: Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]

PROVIDER: PRJNA794837 | ENA |

REPOSITORIES: ENA

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Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]

Project description:The mammalian brain can be divided into distinct structural and functional regions to perform a variety of diverse functions, but during normal aging, exactly how each region is affected, and the information interaction changes between different regions, remains largely unknown. To gain a better insight into these processes, here we generate a single-cell spatial transcriptomic (ST) atlas of young and old mice brains involving cerebrum, brain stem and fiber tracts regions. Based on the unbiased classification of spatial molecular atlas, 27 distinguished brain spatial domains were obtained, which are similar to known anatomical regions, but slightly different. Through differential expression analysis and gene set enrichment analysis (GSEA), we identified aging-related genes and pathways that vary in a coordinated or opposite manner across regions. Combined with single-cell transcriptomic data, we characterized the spatial distribution of cell types, identified an up-regulated gene Ifi27 across regions and cell types in VIS region. Through ligand-receptor interaction analysis, we identified all possible information interaction changes between regions with aging. In summary, we establish a brain spatial molecular atlas (accessible online at https:) to provide a rich resource of spatially differentially expressed genes and information interaction, which may help to understand aging and provide novel insights into the molecular mechanism of brain aging.

2024-02-20 | GSE193107 | GEO

Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

Project description:Here, we have developed a novel methodology called IRIS (Imaging Reconstruction using Indexed Sequencing) that enables cost-effective spatial transcriptomics profiling without relying on optical imaging. Through neighborhood interaction-based reconstruction, IRIS allows extensive analysis of large tissue sections and many replicates with adjustable mapping resolution at only a fraction of the cost of other commercial platforms. With the IRIS platform, we reconstructed a large area spatial area with two whole mouse brain coronal sections. Moreover, we also created a spatially resolved transcriptome atlas of the mouse brain and identified aging-associated changes in gene expression and spatial organization across various brain cell types. Further analysis of cell-cell interaction changes identified aging-associated foci in white matter regions enriched with inflammatory subtypes of microglia and oligodendrocytes. Overall, the IRIS methodology cost-effective and ease-of-use approach makes it broadly applicable to the studies of spatial gene expression changes in various systems.

2024-09-12 | GSE270383 | GEO

Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

Project description:Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

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Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (spatial transcriptomics)

Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".

2024-04-22 | E-MTAB-13991 | biostudies-arrayexpress

Single-cell transcriptomic profiling of the aging mouse brain

Project description:The mammalian brain is complex, with multiple cell types performing a variety of diverse functions, but exactly how each cell type is affected in aging remains largely unknown. Here we performed a single-cell transcriptomic analysis of young and old mouse brains. We provide comprehensive datasets of aging-related genes, pathways and ligand–receptor interactions in nearly all brain cell types. Our analysis identified gene signatures that vary in a coordinated manner across cell types and gene sets that are regulated in a cell-type specific manner, even at times in opposite directions. These data reveal that aging, rather than inducing a universal program, drives a distinct transcriptional course in each cell population, and they highlight key molecular processes, including ribosome biogenesis, underlying brain aging. Overall, these large-scale datasets provide a resource for the neuroscience community that will facilitate additional discoveries directed towards understanding and modifying the aging process.

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Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (scRNA-seq)

Project description:Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (scRNA-seq)

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Spatial transcriptomics of the mouse brain across three age groups

Project description:Aging is a key driver of cognitive decline and the predominant risk factor for several neurodegenerative diseases. Recent behavioral studies as well as structural and functional MRI data suggest that aging does not impact the brain in a uniform manner but follows region- and age-specific trajectories. Yet so far, quantitative analyses of the molecular dynamics in the aging brain have been limited to few regions at low temporal resolution. Here we use the 10X Visium platform to perform spatial transcriptomics (Spatial-seq) of equivalent coronal sections of the mouse brain at young (6 months), middle (18 months) and old (21 months) age.

2023-04-17 | GSE212903 | GEO

Single-cell transcriptomic profiling of the aging mouse brain

Project description:Single-cell transcriptomic profiling of the aging mouse brain

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Spatial transcriptomic analysis of Nf1+/- mouse brain

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Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (scRNA-seq)

Project description:These data were used in the scRNA-seq analysis of the article titled \\"Steroids-producing adrenocortical nodules: a novel two-layered structure as a precursor lesion of cortisol-producing adenoma\\".

2023-12-28 | E-MTAB-13615 | biostudies-arrayexpress

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