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geomx  (Complete Genomics Inc)


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    Complete Genomics Inc geomx
    Geomx, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 99/100, based on 472 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/high+resolution+slide+seq+spatial+transcriptomics+map/Stereo-seq+Transcriptomics+Set+for+FFPE/pmc11744978-17-13-17
    Average 99 stars, based on 472 article reviews
    geomx - by Bioz Stars, 2026-10
    99/100 stars

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    Related Articles

    Transcriptomics:

    Article Title: A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain
    Article Snippet: MERSCOPE Cell Boundary Staining Kit , Vizgen , Cat# 10400118. .. Stereo-seq Transcriptomics T kit v1.3 , STOmics , Cat# 211KT13114-CG. .. Stereo-seq 16 Barcode Library Preparation Kit , STOmics , Cat # 111KL160-CG.

    Expressing:

    Article Title: Functional and Genetic Analyses Unveil the Implication of hoxa4a in Zebrafish Craniofacial Development
    Article Snippet: .. Analysis of hoxa4a expression patterns during early zebrafish embryogenesis was conducted using the Spatial Transcript Omics Database (STOmics DB) [20], incorporating both single-cell RNA sequencing (scRNA-seq) and spatial transcriptomic (stereo-seq) datasets. ..

    Single Cell:

    Article Title: Functional and Genetic Analyses Unveil the Implication of hoxa4a in Zebrafish Craniofacial Development
    Article Snippet: .. Analysis of hoxa4a expression patterns during early zebrafish embryogenesis was conducted using the Spatial Transcript Omics Database (STOmics DB) [20], incorporating both single-cell RNA sequencing (scRNA-seq) and spatial transcriptomic (stereo-seq) datasets. ..

    Article Title: Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching.
    Article Snippet: Similar to the evolutionary history of all species on Earth, the developmental lineage history of all cells in a multicellular organism is stored in a phylogenetic tree.. Mapping the zygote-to-adult developmental cell phylogeny of a complex organism is of tremendous value but technically challenging.. We here developed e-SMALT, a powerful cell lineage tracing system integrated with single-cell RNA sequencing, in Arabidopsis thaliana to record the zygote-to-adult developmental lineages of two plant individuals.

    RNA Sequencing:

    Article Title: Functional and Genetic Analyses Unveil the Implication of hoxa4a in Zebrafish Craniofacial Development
    Article Snippet: .. Analysis of hoxa4a expression patterns during early zebrafish embryogenesis was conducted using the Spatial Transcript Omics Database (STOmics DB) [20], incorporating both single-cell RNA sequencing (scRNA-seq) and spatial transcriptomic (stereo-seq) datasets. ..

    Transformation Assay:

    Article Title: Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching.
    Article Snippet: Similar to the evolutionary history of all species on Earth, the developmental lineage history of all cells in a multicellular organism is stored in a phylogenetic tree.. Mapping the zygote-to-adult developmental cell phylogeny of a complex organism is of tremendous value but technically challenging.. We here developed e-SMALT, a powerful cell lineage tracing system integrated with single-cell RNA sequencing, in Arabidopsis thaliana to record the zygote-to-adult developmental lineages of two plant individuals.

    other:

    Article Title: RegFormer: a single-cell foundation model powered by gene regulatory hierarchies.
    Article Snippet: We acknowledge the Stomics Cloud platform (https://cloud.stomics.tech/) for providing GPU computational resources.

    Sequencing:

    Article Title: Adult regenerative defects arise from discordant scaling of signal dependent growth and patterning
    Article Snippet: .. All subsequent steps, including cryosectioning, Stereo-seq library preparation, sequencing, and raw data processing, were performed at the BGI facility (Riga, Latvia) in collaboration with BGI, supported by a STOmics Grant awarded to E. Tanaka. .. All subsequent steps, including cryosectioning, Stereo-seq library preparation, sequencing, and raw data processing, were performed at the BGI facility (Riga, Latvia) in collaboration with BGI, supported by a STOmics Grant awarded to E. Tanaka.

    H&E Stain:

    Article Title: Spatial transcriptomic profiling of porcine tissue microarray detecting subclinical circovirus infection
    Article Snippet: .. The first section was subjected to H&E staining for histological evaluation, while the second was mounted directly onto a Stereo-seq chip N Slide V1.0 (STOmics, Cat. No. 210CN114). .. Subsequent processing was performed according to the Stereo-seq Transcriptomics Set for FFPE User Manual (Document No. STUM-TT004) using the Stereo-seq Transcriptomics N Kit V1.0 (Cat. No. 211KN114) and Stereo-seq 16 Barcode Library Preparation Kit V1.0 (Cat. No. 111KL160).



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    Spatial Transcriptomics Inc high resolution slide seq spatial transcriptomics map
    Fig. 1 | Single-cell and spatial <t>transcriptomics</t> of cardiac and ileum tissue of reovirus-infected neonatal mice. a, Experiment and analysis workflow. Four- day-old neonatal mice weighing 3 g per pup were infected (per os) with reovirus T1L. Neonatal mice infected with 1× PBS were used as mock controls. Ileum tissue (1 dpi and 4 dpi) and heart tissues (4 dpi, 7 dpi and 10 dpi) were assayed and used for scRNA-seq and spatial transcriptomics. b, UMAP plot of 31,684 single-cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi (one animal per condition), clustered by gene expression and colored by cell type (left). UMAP plots showing cardiac cell type clusters across samples for the heart scRNA-seq data (right). c, 8,243 spatial transcriptomes of cardiac tissue sections from mock-infected and reovirus-infected mice at 4 dpi and 7 dpi (one animal per condition). H&E-stained image of reovirus-infected myocarditic
    High Resolution Slide Seq Spatial Transcriptomics Map, supplied by Spatial Transcriptomics Inc, 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/high+resolution+slide+seq+spatial+transcriptomics+map/seq+slide/pm36970396-158-20-22
    Average 86 stars, based on 1 article reviews
    high resolution slide seq spatial transcriptomics map - by Bioz Stars, 2026-10
    86/100 stars
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    Fig. 1 | Single-cell and spatial transcriptomics of cardiac and ileum tissue of reovirus-infected neonatal mice. a, Experiment and analysis workflow. Four- day-old neonatal mice weighing 3 g per pup were infected (per os) with reovirus T1L. Neonatal mice infected with 1× PBS were used as mock controls. Ileum tissue (1 dpi and 4 dpi) and heart tissues (4 dpi, 7 dpi and 10 dpi) were assayed and used for scRNA-seq and spatial transcriptomics. b, UMAP plot of 31,684 single-cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi (one animal per condition), clustered by gene expression and colored by cell type (left). UMAP plots showing cardiac cell type clusters across samples for the heart scRNA-seq data (right). c, 8,243 spatial transcriptomes of cardiac tissue sections from mock-infected and reovirus-infected mice at 4 dpi and 7 dpi (one animal per condition). H&E-stained image of reovirus-infected myocarditic

    Journal: Nature cardiovascular research

    Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

    doi: 10.1038/s44161-022-00138-1

    Figure Lengend Snippet: Fig. 1 | Single-cell and spatial transcriptomics of cardiac and ileum tissue of reovirus-infected neonatal mice. a, Experiment and analysis workflow. Four- day-old neonatal mice weighing 3 g per pup were infected (per os) with reovirus T1L. Neonatal mice infected with 1× PBS were used as mock controls. Ileum tissue (1 dpi and 4 dpi) and heart tissues (4 dpi, 7 dpi and 10 dpi) were assayed and used for scRNA-seq and spatial transcriptomics. b, UMAP plot of 31,684 single-cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi (one animal per condition), clustered by gene expression and colored by cell type (left). UMAP plots showing cardiac cell type clusters across samples for the heart scRNA-seq data (right). c, 8,243 spatial transcriptomes of cardiac tissue sections from mock-infected and reovirus-infected mice at 4 dpi and 7 dpi (one animal per condition). H&E-stained image of reovirus-infected myocarditic

    Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

    Techniques: Infection, Gene Expression, Staining

    Fig. 3 | Cytotoxic T cells recruited by inflamed endothelial cells induce pyroptosis in myocarditic tissue. a, UMAP plot of 9,786 single-cell endothelial cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by endothelial cell subtype clusters (phenotypes) (top) and condition (bottom). b, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for endothelial cell subtypes. c, UMAP plot showing the expression of genes upregulated in Cxcl9-high endothelial cells. d, Spatial transcriptomic maps of cardiac tissue from reovirus infected hearts at 7 dpi showing gene module scores calculated for four GO terms enriched in Cxcl9-high endothelial cells. e, UMAP plot of 2,205 single-cell T cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by T cell subtype clusters (top) and condition (bottom). f, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for T cell subtypes. g, UMAP plot showing the expression of genes upregulated in cytotoxic T cells from myocarditic heart at 7 dpi. h, Spatial transcriptomics maps of cardiac tissue from reovirus infected hearts at 7 dpi

    Journal: Nature cardiovascular research

    Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

    doi: 10.1038/s44161-022-00138-1

    Figure Lengend Snippet: Fig. 3 | Cytotoxic T cells recruited by inflamed endothelial cells induce pyroptosis in myocarditic tissue. a, UMAP plot of 9,786 single-cell endothelial cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by endothelial cell subtype clusters (phenotypes) (top) and condition (bottom). b, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for endothelial cell subtypes. c, UMAP plot showing the expression of genes upregulated in Cxcl9-high endothelial cells. d, Spatial transcriptomic maps of cardiac tissue from reovirus infected hearts at 7 dpi showing gene module scores calculated for four GO terms enriched in Cxcl9-high endothelial cells. e, UMAP plot of 2,205 single-cell T cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by T cell subtype clusters (top) and condition (bottom). f, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for T cell subtypes. g, UMAP plot showing the expression of genes upregulated in cytotoxic T cells from myocarditic heart at 7 dpi. h, Spatial transcriptomics maps of cardiac tissue from reovirus infected hearts at 7 dpi

    Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

    Techniques: Infection, Expressing

    Fig. 4 | Myocarditic regions and the border zone have distinct transcriptomic profiles and cell-type-specific signatures. a, Spatial transcriptomics map of cardiac tissue section from reovirus-infected mice at 7 dpi colored by spot clusters representing transcriptionally distinct tissue regions. b, Spatial transcriptomics maps of cardiac tissue sections from reovirus-infected mice at 7 dpi showing the expression of differentially expressed genes of interest in the myocarditic and the border zone. c, Changes in average predicted cell type proportions across the infected ventricle, for cell types enriched in the myocarditic region and the border zone. d, UMAP plot of 502 single-cell cardiomyocyte cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by myocyte cell subtype (phenotypes) (left) and condition (right). e, Heat map showing the top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for cardiomyocyte cell subtypes. f, Venn diagram showing myocyte-specific genes

    Journal: Nature cardiovascular research

    Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

    doi: 10.1038/s44161-022-00138-1

    Figure Lengend Snippet: Fig. 4 | Myocarditic regions and the border zone have distinct transcriptomic profiles and cell-type-specific signatures. a, Spatial transcriptomics map of cardiac tissue section from reovirus-infected mice at 7 dpi colored by spot clusters representing transcriptionally distinct tissue regions. b, Spatial transcriptomics maps of cardiac tissue sections from reovirus-infected mice at 7 dpi showing the expression of differentially expressed genes of interest in the myocarditic and the border zone. c, Changes in average predicted cell type proportions across the infected ventricle, for cell types enriched in the myocarditic region and the border zone. d, UMAP plot of 502 single-cell cardiomyocyte cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by myocyte cell subtype (phenotypes) (left) and condition (right). e, Heat map showing the top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for cardiomyocyte cell subtypes. f, Venn diagram showing myocyte-specific genes

    Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

    Techniques: Infection, Expressing