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10X Genomics xenium in situ
Xenium In Situ, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transcriptome+data/data+spatial+transcriptomic/pmc12956572-205-14-25
Average 86 stars, based on 1 article reviews
xenium in situ - by Bioz Stars, 2026-09
86/100 stars

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Spatial Transcriptomics:

Article Title: Single-cell multiomics gene regulatory landscape reveals impaired spermatogonial stem cells and macrophage-driven inflammaging during testicular aging.
Article Snippet: 29 Testicular aging is a key driver of declining male reproductive health, but a comprehensive 30 understanding of its underlying epigenetic drivers is lacking.. To address this, we construct a 31 multiomics aging atlas by integrating single-cell RNA sequencing, single-cell assay for 32 transposase-accessible chromatin sequencing (scATAC-seq), and spatial transcriptomics of 33 young and aged mouse testes.. Our analysis reveals that altered chromatin accessibility 34 accompanies transcriptional dysregulation and identifies spermatogonial stem cells (SSCs) as 35 the most epigenetically vulnerable population.

Sequencing:

Article Title: Single-cell multiomics gene regulatory landscape reveals impaired spermatogonial stem cells and macrophage-driven inflammaging during testicular aging.
Article Snippet: 29 Testicular aging is a key driver of declining male reproductive health, but a comprehensive 30 understanding of its underlying epigenetic drivers is lacking.. To address this, we construct a 31 multiomics aging atlas by integrating single-cell RNA sequencing, single-cell assay for 32 transposase-accessible chromatin sequencing (scATAC-seq), and spatial transcriptomics of 33 young and aged mouse testes.. Our analysis reveals that altered chromatin accessibility 34 accompanies transcriptional dysregulation and identifies spermatogonial stem cells (SSCs) as 35 the most epigenetically vulnerable population.

Article Title: Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
Article Snippet: .. To minimize batch effects caused by differences in sequencing platforms and methodologies, all single-cell and spatial transcriptomic data were obtained exclusively from the 10x Genomics and 10x Visium platforms. ..

Gene Expression:

Article Title: Single-cell multiomics gene regulatory landscape reveals impaired spermatogonial stem cells and macrophage-driven inflammaging during testicular aging.
Article Snippet: 29 Testicular aging is a key driver of declining male reproductive health, but a comprehensive 30 understanding of its underlying epigenetic drivers is lacking.. To address this, we construct a 31 multiomics aging atlas by integrating single-cell RNA sequencing, single-cell assay for 32 transposase-accessible chromatin sequencing (scATAC-seq), and spatial transcriptomics of 33 young and aged mouse testes.. Our analysis reveals that altered chromatin accessibility 34 accompanies transcriptional dysregulation and identifies spermatogonial stem cells (SSCs) as 35 the most epigenetically vulnerable population.

Single Cell:

Article Title: Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.
Article Snippet: .. To minimize batch effects caused by differences in sequencing platforms and methodologies, all single-cell and spatial transcriptomic data were obtained exclusively from the 10x Genomics and 10x Visium platforms. ..

Article Title: The Role of Tumor Necrosis Factor Signaling in Atherosclerosis and Stroke
Article Snippet: .. To characterise TNF signaling within atherosclerotic plaques, we analysed two publicly available datasets: (i) an integrated single-cell RNA-sequencing (scRNA-seq) atlas of 259,116 cells from human carotid, coronary, and femoral plaques (73 donors), and (ii) Xenium (10x Genomics) spatial transcriptomic data comprising 120,164 cells from carotid endarterectomy specimens with pathologist-annotated subregions (12 donors). ..

In Situ:

Article Title: SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.
Article Snippet: .. Spatial transcriptomic profiling with Xenium In Situ platform Slides were prepared following the manufacturer’s instructions and workflow for FFPE tissue samples (CG000578 Rev A; 10x Genomics). .. A 5-μm section from the tissue block containing the same paired tonsil and adenoid samples (one from INF donor and one from VAC donor) used for immunofluorescence were carefully attached to the sample area on a Xenium slide (Histoserv, MD).

Article Title: An antioxidant therapy elicits distinct transcriptome responses in 22q11-deleted upper layer cortical projection neurons.
Article Snippet: .. To assess L 2/3 PN transcriptional responses that underlie NAC’s therapeutic effects in vivo, we first established that spatial transcriptomic RNA quantification in situ (10X Genomics Xenium) securely identifies L 2/3 PNs and their neighbors, thus ensuring that transcriptional states can be assessed in intact cortices of early post-natal WT, LgDel, LgDel + NAC and WT + NAC L 2/3 mice. ..

Article Title: Won't you be my neighbor? Control of the immune response by stromal and immune cell microenvironments within the lymph node.
Article Snippet: Efficacious immune responses require the coordinated encounter of rare antigen-specific adaptive lymphocytes with their cognate innate antigen-presenting cells (APCs) in space and time.. This spatiotemporal problem of immunity is solved by secondary lymphoid organs, such as lymph nodes (LNs), which coordinate adaptive immune responses by recruiting APCs and lymphocytes into close juxtaposition with tissue antigens drained from the periphery.. A central tenet to the overall function of the LN is the spatial organization of leukocytes into discrete microenvironments orchestrated by the mesenchymal and endothelial cells, collectively termed LN stromal cells (LNSCs).

Formalin-fixed Paraffin-Embedded:

Article Title: SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.
Article Snippet: .. Spatial transcriptomic profiling with Xenium In Situ platform Slides were prepared following the manufacturer’s instructions and workflow for FFPE tissue samples (CG000578 Rev A; 10x Genomics). .. A 5-μm section from the tissue block containing the same paired tonsil and adenoid samples (one from INF donor and one from VAC donor) used for immunofluorescence were carefully attached to the sample area on a Xenium slide (Histoserv, MD).

In Vivo:

Article Title: An antioxidant therapy elicits distinct transcriptome responses in 22q11-deleted upper layer cortical projection neurons.
Article Snippet: .. To assess L 2/3 PN transcriptional responses that underlie NAC’s therapeutic effects in vivo, we first established that spatial transcriptomic RNA quantification in situ (10X Genomics Xenium) securely identifies L 2/3 PNs and their neighbors, thus ensuring that transcriptional states can be assessed in intact cortices of early post-natal WT, LgDel, LgDel + NAC and WT + NAC L 2/3 mice. ..

RNA sequencing:

Article Title: The Role of Tumor Necrosis Factor Signaling in Atherosclerosis and Stroke
Article Snippet: .. To characterise TNF signaling within atherosclerotic plaques, we analysed two publicly available datasets: (i) an integrated single-cell RNA-sequencing (scRNA-seq) atlas of 259,116 cells from human carotid, coronary, and femoral plaques (73 donors), and (ii) Xenium (10x Genomics) spatial transcriptomic data comprising 120,164 cells from carotid endarterectomy specimens with pathologist-annotated subregions (12 donors). ..



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a) Log 2 ([elevated temperature/control] average total accumulation) of metabolic categories (n≥3) at six different seed developmental stages. b) Untargeted metabolomic data statistical analysis. c) Differentially accumulated metabolic features during seed development. d) Number of major metabolic categories (Flavonoids, Cinnamic acids and derivatives, and Glucosinolates) induced by elevated temperature at each seed developmental stage. e) Transcriptomic data statistical analysis. f) Differentially expressed genes during seed development. g) Percentages of genes coding for enzymes putatively involved in specialized metabolite modifications (Acyltransferases, Glycosyltransferases, Hydroxylases and Methyltransferases) induced, and repressed, at each seed developmental stage by elevated temperature.

Journal: bioRxiv

Article Title: Elevated temperature drives the biosynthesis of novel acylated glucosinolates in Arabidopsis thaliana seeds

doi: 10.64898/2026.06.03.729804

Figure Lengend Snippet: a) Log 2 ([elevated temperature/control] average total accumulation) of metabolic categories (n≥3) at six different seed developmental stages. b) Untargeted metabolomic data statistical analysis. c) Differentially accumulated metabolic features during seed development. d) Number of major metabolic categories (Flavonoids, Cinnamic acids and derivatives, and Glucosinolates) induced by elevated temperature at each seed developmental stage. e) Transcriptomic data statistical analysis. f) Differentially expressed genes during seed development. g) Percentages of genes coding for enzymes putatively involved in specialized metabolite modifications (Acyltransferases, Glycosyltransferases, Hydroxylases and Methyltransferases) induced, and repressed, at each seed developmental stage by elevated temperature.

Article Snippet: Untargeted metabolomic raw data (.mzXML) for both negative and positive ESI modes, and metadata have been deposited at the MassiVE data repository portal with the following identifiers: The transcriptomic RNA-Seq raw data (FASTQ) have been deposited at the National Center for Biotechnology Information (NCBI) Transcriptome Shotgun Assembly Sequence Database (TSA) with BioProject identification PRJNA1344327.

Techniques: Control, Metabolomic