geomx dsp Search Results


geomx dsp immuno-oncology protein panel assay  (Visiopharm AS)
90
Visiopharm AS geomx dsp immuno-oncology protein panel assay
Geomx Dsp Immuno Oncology Protein Panel Assay, supplied by Visiopharm AS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/geomx+dsp/pm39635525-272-4-13?v=Visiopharm+AS
Average 90 stars, based on 1 article reviews
geomx dsp immuno-oncology protein panel assay - by Bioz Stars, 2026-08
90/100 stars
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geomx digital spatial profiling (dsp)  (Johns Hopkins HealthCare)
90
Johns Hopkins HealthCare geomx digital spatial profiling (dsp)
(A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and <t>GeoMx</t> datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.
Geomx Digital Spatial Profiling (Dsp), supplied by Johns Hopkins HealthCare, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/geomx+dsp/bio_rxiv__2025__07__11__664335-46-0-20?v=Johns+Hopkins+HealthCare
Average 90 stars, based on 1 article reviews
geomx digital spatial profiling (dsp) - by Bioz Stars, 2026-08
90/100 stars
  Buy from Supplier
geomx dsp  (RStudio)
90
RStudio geomx dsp
(A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and <t>GeoMx</t> datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.
Geomx Dsp, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/geomx+dsp/10__1158_slash_1078___0432__ccr___23___0827-114-3-11?v=RStudio
Average 90 stars, based on 1 article reviews
geomx dsp - by Bioz Stars, 2026-08
90/100 stars
  Buy from Supplier
geomx dsp  (Azenta)
86
Azenta geomx dsp
(A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and <t>GeoMx</t> datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.
Geomx Dsp, supplied by Azenta, 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/geomx+dsp/bio_rxiv__64898__2025__12__10__693392-386-5-10?v=Azenta
Average 86 stars, based on 1 article reviews
geomx dsp - by Bioz Stars, 2026-08
86/100 stars
  Buy from Supplier

Image Search Results


(A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and GeoMx datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.

Journal: bioRxiv

Article Title: Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis

doi: 10.1101/2025.07.11.664335

Figure Lengend Snippet: (A) Proportional Venn diagram showing the overlap of DEGs between Visium (FindAllMarkers) and GeoMx datasets (all compartments). Fourteen DEGs were consistently differentially regulated in myocarditis relative to controls across both platforms. Corresponding fold changes for these overlapping genes are shown in the heatmap below. (B) Proportional Venn diagram comparing DEGs identified only in cardiomyocyte-stained segments (TNNI3⁺CD45⁻) and leukocyte depleted, cardiomyocyte-enriched genes (Visium), revealing ten shared DEGs between both datasets. Fold change values for these overlapping genes are shown in the heatmap. Color intensity in the heatmaps reflects the magnitude of absolute fold change values for each gene. Genes shown were filtered based on adjusted p-value of at least < 0.01 and exhibited consistent directionality of effect across platforms. Heatmap values for upregulated genes with FC higher than 4 were capped to this maximum value to aid visualization (see Supplementary Table 10 for values). (C) Chord plot illustrating inferred ligand– receptor interactions derived from differentially expressed genes in cardiomyocyte-enriched regions from both experimental techniques, focusing on overlapping antigen presentation–related genes, weighted by expression confidence. Arcs represent predicted interactions between ligands and immune receptors. Interactions were inferred using the OmniPath ligand–receptor database, and visualized using network-based filtering of curated, directional signaling interactions. Bolded genes represent overlapped genes present in OmniPath, between the two orthogonal experimental techniques.

Article Snippet: GeoMx Digital Spatial Profiling (DSP) was subsequently performed in the Spatial Cancer Research Immunobiology & Therapeutics (SCRIPT) Laboratory and the Johns Hopkins Experimental and Computational Genomics Core to validate transcriptional findings and enable spatially resolved whole-transcriptome gene expression profiling in cardiac tissue.

Techniques: Staining, Derivative Assay, Immunopeptidomics, Expressing

(A) Representative immunohistochemical (IHC) micrograph of endomyocardial biopsy (EMBx) tissue highlighting cardiomyocytes (TNNI3⁺, yellow), leukocytes (CD45⁺, red), and nuclei (Syto83, green). (B) Representative segmentation overlay into three compartments: cardiomyocytes (TNNI3⁺CD45⁻, yellow), leukocytes (TNNI3⁻CD45⁺, red), and non-myocytes (TNNI3⁻CD45⁻, blue), for IHC-guided transcriptomics (GeoMx DSP). (C) Volcano plot showing all DEGs between controls and myocarditis in all segments, (D) TNNI3 + CD45 - cardiomyocytes, (E) TNNI3 - CD45 + leukocytes, and (F) TNNI3 - CD45 - non-myocytes/stromal cells. DEGs were computed using Q3 normalization followed by linear mixed-effects modeling with a FC threshold > 1.5 and an adjusted p < 0.05. For non-myocyte comparisons (F), unadjusted p -values were used due to lower segment counts and limited detection sensitivity.

Journal: bioRxiv

Article Title: Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis

doi: 10.1101/2025.07.11.664335

Figure Lengend Snippet: (A) Representative immunohistochemical (IHC) micrograph of endomyocardial biopsy (EMBx) tissue highlighting cardiomyocytes (TNNI3⁺, yellow), leukocytes (CD45⁺, red), and nuclei (Syto83, green). (B) Representative segmentation overlay into three compartments: cardiomyocytes (TNNI3⁺CD45⁻, yellow), leukocytes (TNNI3⁻CD45⁺, red), and non-myocytes (TNNI3⁻CD45⁻, blue), for IHC-guided transcriptomics (GeoMx DSP). (C) Volcano plot showing all DEGs between controls and myocarditis in all segments, (D) TNNI3 + CD45 - cardiomyocytes, (E) TNNI3 - CD45 + leukocytes, and (F) TNNI3 - CD45 - non-myocytes/stromal cells. DEGs were computed using Q3 normalization followed by linear mixed-effects modeling with a FC threshold > 1.5 and an adjusted p < 0.05. For non-myocyte comparisons (F), unadjusted p -values were used due to lower segment counts and limited detection sensitivity.

Article Snippet: GeoMx Digital Spatial Profiling (DSP) was subsequently performed in the Spatial Cancer Research Immunobiology & Therapeutics (SCRIPT) Laboratory and the Johns Hopkins Experimental and Computational Genomics Core to validate transcriptional findings and enable spatially resolved whole-transcriptome gene expression profiling in cardiac tissue.

Techniques: Immunohistochemical staining