CRISP enables comparisons of image-based spatial transcriptomic segmentation quality across ten organs
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE328169 | GEO | 2026/04/20
REPOSITORIES: GEO
Similar Datasets
Project description:CRISP enables comparisons of image-based spatial transcriptomic segmentation quality across ten organs
| PRJNA1454030 | ENA
Project description:This study examines the effect of four different image segmentation methods on the precision of the data. Keywords: other
2004-03-16 | GSE1054 | GEO
Project description:BackgroundAging is a complex biological process characterized by progressive molecular alterations across multiple organ systems, significantly influencing disease susceptibility and mortality. Unraveling molecular interactions driving aging is crucial for interventions promoting healthy aging and mitigating senescence. However, the systemic mechanisms governing both inter-organ interactions and organ-specific aging trajectories remain incompletely characterized.MethodsTo investigate the molecular dynamics of aging, we conducted a systematic multi-omics analysis of 400 tissue samples collected from 10 organs (brain, heart, intestine, kidney, liver, lung, muscle, skin, spleen, and stomach) in mice at four distinct life stages: 4, 8, 12, and 20 months (from youth to elderly). Proteomic profiling was performed using data-independent acquisition (DIA) technology, while metabolomic analysis was performed in both positive and negative ion modes. Differential expression analysis of proteins and metabolites was employed to construct a comprehensive multi-organ aging dataset. ResultsProteomic profiling across ten organs at four age stages identified a total of 14,763 protein groups (PGs). Of these, 18 proteins, including Ighm, C4b, and Hpx, exhibited consistent age-related differential expression patterns across all ten organs. Functional enrichment analysis highlighted the humoral immune response as a primary driver of age-related expression changes. Additionally, this study mapped a set of age-unique proteins, such as Hp, Egf, and Arg, with distinct expression patterns in aging organs. Metabolic analysis identified 3,779 metabolites, with key aging-related metabolites such as NAD+, inosine, xanthine, and hypoxanthine showing significant expression changes across multiple organs. Pathway enrichment analysis revealed consistent alterations in purine metabolism, pyrimidine metabolism, riboflavin metabolism, and nicotinate/nicotinamide metabolism during multi-organ aging.ConclusionsThis study provides a multi-omics atlas of multi-organ aging, revealing both intra- and inter-organ similarities and heterogeneities. These findings offer valuable insights into the molecular mechanisms underlying geriatric health decline and serve as a foundational resource for organism-systematic early warning and targeted interventions against aging-associated pathologies.
2025-08-27 | PXD047296 | Pride
Project description:Eubacterium limosum ATCC 8486 makes acetate and butyrate from various substrates and is found in the human intestine. The proteome of choline -grown Eubacterium limosum was obtained in order to identify enzymes required for growth on choline, in particular to identify components that are unique to growth on choline in comparison to other substrates for acetogenesis, such as lactic acid, L-carnitine, or proline betaine. Choline is converted to trimethylamine (TMA) by certain members of the gut microbiome. Subsequent liver metabolism of TMA is now tied to progression of cardiovascular disease. Demethylation of choline is observed during growth of Eubacterium limosum on this substrate, and does not produce TMA. Choline demethylation by organisms like Eubacterium limosum could lessen TMA production in the gut, thereby lessening the propensity towards atherosclerosis caused by metabolism of TMA in the body. This proteome led to discovery of a phosphocholine:tetrahydrofolate methyltransferase system. The key choline demethylating enzyme is a member of the widespread TMA methyltransferase protein superfamily.
2025-06-16 | PXD033467 | Pride
Project description:Eubacterium limosum ATCC 8486 makes acetate and butyrate from various substrates and is found in the human intestine. The proteome of L-carnitine-grown Eubacterium limosum was obtained in order to identify enzymes required for growth on L-carnitine, in particular to identify components that are unique to growth on L-carnitine in comparison to other substrates for acetogenesis, such as lactic acid. L-carnitine and derviatives are converted to trimethylamine (TMA) by certain members of the gut microbiome, metabolism of TMA is now tied to progression of cardiovascular disease. Demethylation of carnitine is observed during growth of Eubacterium limosum on this substrate, and does not produce TMA. Carnitine demethylation by organisms like Eubacterium limosum could lessen TMA production in the gut, thereby lessening the propensity towards atherorsclerosis caused by metabolism of TMA in the body. The carnitine proteome led to the description of a carnitine:tetrahydrofolate methyltransferase system. The key carnitine demethylating enzyme is a member of the widespread TMA methyltransferase protein superfamily.
2020-06-19 | PXD013961 | Pride
Project description:<p>The complexity of the aging process, encompassing numerous organs and systems, poses a significant challenge in identifying and targeting key factors that drive age-related decline. The multi-organ synchronous molecular intricacies underlying natural aging remain elusive. Here we presented a data resource for proteomics and metabolomics analyses on ten organs (brain, heart, intestine, kidney, liver, lung, muscle, skin, spleen and stomach) of mice spanning from youth to aging (4, 8, 12 and 20 months, n = 10). We detected and quantified 14,763 protein groups (PGs) and 4,779 metabolites across the ten organs. We found immunoregulation was deeply involved in multi-organ aging. Specifically, 18 immune-related proteins including Ighm showed significant expression changes in all ten organs. Besides, aging organs also expressed age-attributed proteins such as App, Plg and Saa1. Our study revealed that age-related metabolite changes are primarily concentrated in purine, pyrimidine and nicotinate-nicotinamide metabolism, and further constructed a differential proteins-metabolites network. These data highlight the dynamic molecular changes during organ aging, offering insights into geriatric health decline.</p>
2025-08-29 | MTBLS10642 | MetaboLights
Project description:Eubacterium limosum ATCC 8486 makes acetate and butyrate from various substrates and is found in the human intestine. The proteome of gamma-butyrobetaine -grown Eubacterium limosum was obtained in order to identify enzymes required for growth on gamma-butyrobetaine, in particular to identify components that are unique to growth on gamma-butyrobetaine in comparison to other substrates for acetogenesis, such as lactic acid, L-carnitine, or proline betaine. Gamma-butyrobetaine is converted to trimethylamine (TMA) by certain members of the gut microbiome. Subsequent liver metabolism of TMA is now tied to progression of cardiovascular disease. Demethylation of gamma-butyrobetaine is observed during growth of Eubacterium limosum on this substrate, and does not produce TMA. Gamma-butyrobetaine demethylation by organisms like Eubacterium limosum could lessen TMA production in the gut, thereby lessening the propensity towards atherosclerosis caused by metabolism of TMA in the body. This proteome led to discovery of gamma-butyrobetaine:tetrahydrofolate methyltransferase system. The key gamma-butyrobetaine demethylating enzyme is a member of the widespread TMA methyltransferase protein superfamily.
2021-11-04 | PXD020152 | Pride
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2022-02-02 | MSV000088772 | GNPS
Project description:Metabolites (aqueous & organic) were extracted from mouse tissues and tissues' contents (SI duodenum, SI jejunum, SI ileum, cecum, large intestine, small intestine, contents, cecum contents, large intestine contents, heart, liver, and quad) and were run by LC-MS, C8 in positive mode.
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