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Spatial Transcriptomics Inc geomx dsp spatial transcriptomics technology
Geomx Dsp Spatial Transcriptomics Technology, 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/spatial+transcriptomics+geomx/3d+spatial+technology+transcriptomics/pmc12331751-162-4-6
Average 86 stars, based on 1 article reviews
geomx dsp spatial transcriptomics technology - by Bioz Stars, 2026-10
86/100 stars

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Related Articles

Selection:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Immunohistochemistry:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Multiplex Assay:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Immunofluorescence:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Staining:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Sequencing:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

RNA sequencing:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Spatial Transcriptomics:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Article Title: CXCL16 Producing Tumor Clones Are Shaping Immunosuppressive Microenvironment in Squamous Cell Carcinoma via CXCR6 Regulatory T Cell
Article Snippet: .. Spatial transcriptomics was performed using the GeoMx DSP platform of the whole‐transcriptome atlas (NanoString Technologies, Seattle, WA, USA). .. Tissue sections from formalin‐fixed paraffin‐embedded (FFPE) blocks were mounted on a charged Leica Bond slide.

Article Title: Multi-modal molecular and spatial profiling reveals NNT as a prognostic biomarker in obesity-associated colorectal cancer.
Article Snippet: .. Panels A–B illustrate the individual prognostic impact of TNM stage alone, while panels C–F show the combined analysis integrating NNT expression with TNM staging ◂ Fig. 4 Analysis of NNT expression in obese colorectal cancer (CRC) patients using GeoMx spatial transcriptomics technology. ..

Article Title: Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment
Article Snippet: Spatial Transcriptomics + Proteomics , 2020 , DBiT-seq , 10–50 μm , [ ] . .. Spatial Transcriptomics + Proteomics , 2020 , GeoMx DSP , Single-cell , [ ] . .. Spatial Epigenome + Proteomics , 2020 , OligoFISSEQ , Single-cell , [ ] .

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ ]. ..

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease.
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ 3 ]. ..

Spatial Proteomics:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Single Cell:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

Article Title: Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment
Article Snippet: Spatial Transcriptomics + Proteomics , 2020 , DBiT-seq , 10–50 μm , [ ] . .. Spatial Transcriptomics + Proteomics , 2020 , GeoMx DSP , Single-cell , [ ] . .. Spatial Epigenome + Proteomics , 2020 , OligoFISSEQ , Single-cell , [ ] .

Transcriptomics:

Article Title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures.
Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Sample collection and ethical approval ○ Patient selection ○ Clinical data and analysis • METHOD DETAILS ○ IHC and screening for B-cell aggregation ○ Multiplex immunofluorescence staining and digital image analysis ○ Whole exome sequencing and analysis ○ Bulk RNA-sequencing and analysis ○ Spatial transcriptomics with GeoMx® DSP ○ High-plex spatial proteomics & image analysis ○ Spatial single-cell transcriptomics (Xenium) ○ Immunoglobulin sequencing • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. immuni.2025.09.018. ..

In Silico:

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Hybridization:

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Imaging:

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Polymerase Chain Reaction:

Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues
Article Snippet: Note: Bruker Spatial Biology offers, both, mouse and human whole transcriptome atlases containing probes to detect approximately 22,000 host transcripts. .. The pathogen-specific probes were custom-designed using P. aeruginosa PA14 genomic information , , with a computational in silico preselection filters., Spatial transcriptomics workflow using GeoMx DSP instrument The procedure covers the following steps: Day1 - Slide processing using Bond RxV pipeline and probe library hybridization, Day 2 - GeoMx run consisting of staining of slides with morphology markers, GeoMx imaging, ROI selection, and sample acquisition, Day 3 - PCR-based library preparation, quantification, and sequencing, Day 4 - Data analytics. ..

Expressing:

Article Title: Multi-modal molecular and spatial profiling reveals NNT as a prognostic biomarker in obesity-associated colorectal cancer.
Article Snippet: .. Panels A–B illustrate the individual prognostic impact of TNM stage alone, while panels C–F show the combined analysis integrating NNT expression with TNM staging ◂ Fig. 4 Analysis of NNT expression in obese colorectal cancer (CRC) patients using GeoMx spatial transcriptomics technology. ..

Microscopy:

Article Title: Spatial transcriptomics: a bibliometric analysis with large language model on English literatures
Article Snippet: Table S5: A Comprehensive Report on Predictions for Future Research Directions in Spatial Transcriptomics Using ChatGPT-4o Enhanced Spatial Resolution and Multi-Scale Profiling ⚫ Subcellular and Organelle-Level Profiling: Techniques like spatial-ATAC-seq and SEAM will map chromatin accessibility and metabolic heterogeneity at subcellular scales. .. ⚫ 3D Spatial Transcriptomics: Combining expansion microscopy with RNA capture to study 3D tissue architecture (e.g., liver lobules, brain circuits). ..

Construct:

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ ]. ..

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease.
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ 3 ]. ..

Gene Expression:

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ ]. ..

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease.
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ 3 ]. ..

Functional Assay:

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ ]. ..

Article Title: So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease.
Article Snippet: .. Notably, the 3D spatial transcriptomics technology has constructed the 3D view of gene expression, cell types, and functional states within tissues and organs, revealing spatially continuous structures and biomarkers that are invisible in two-dimensional (2D) slices [ 3 ]. ..



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( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial <t>transcriptomics</t> using <t>GeoMx®</t> <t>DSP:</t> slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .
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( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial <t>transcriptomics</t> using <t>GeoMx®</t> <t>DSP:</t> slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .
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( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial <t>transcriptomics</t> using <t>GeoMx®</t> <t>DSP:</t> slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .
Spatial Transcriptomics Geomx® Platform, supplied by Spatial Transcriptomics Inc, 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/spatial+transcriptomics+geomx/geomx/pm40422184-2-7-3
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Spatial Transcriptomics Inc spatial transcriptomics geomx digital spatial profiler
( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial <t>transcriptomics</t> using <t>GeoMx®</t> <t>DSP:</t> slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .
Spatial Transcriptomics Geomx Digital Spatial Profiler, supplied by Spatial Transcriptomics Inc, 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/spatial+transcriptomics+geomx/geomx/pm40199763-0-1-1
Average 90 stars, based on 1 article reviews
spatial transcriptomics geomx digital spatial profiler - by Bioz Stars, 2026-10
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Bruker Corporation spatial whole transcriptome analysis platform geomx
Representative H&E images of granulomas from A) Case 3, B) Case 2, and C) Case 4 showing a range of granuloma morphology with D) necrotizing granulomas, E) cellular non-necrotizing granulomas, and F) small, lymphocyte rich granulomas as assessed by a pulmonary pathologist using traditional morphological annotation. Regions of interest (ROIs) ( G-K ) were selected based on morphological and fluorescence staining for DNA (blue), CD3 (green), CD68/CD163 (red), and vimentin (yellow). ROIs bordering necrotic (G) granulomas and (H) solid or cellular granulomas were selected in addition to tertiary lymphoid structures (I), lymph node (J), and uninvolved lung (K) for spatial transcriptional profiling using the human whole <t>transcriptome</t> probe set using GeoMx (Bruker).
Spatial Whole Transcriptome Analysis Platform Geomx, supplied by Bruker Corporation, 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/spatial+transcriptomics+geomx/spatial+whole+transcriptome+analysis+platform+geomx/bio_rxiv__2025__03__10__642376-53-22-29
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spatial whole transcriptome analysis platform geomx - by Bioz Stars, 2026-10
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Illumina Inc geomx digital spatial profiling (dsp) cancer whole transcriptome atlas (wta) system
Representative H&E images of granulomas from A) Case 3, B) Case 2, and C) Case 4 showing a range of granuloma morphology with D) necrotizing granulomas, E) cellular non-necrotizing granulomas, and F) small, lymphocyte rich granulomas as assessed by a pulmonary pathologist using traditional morphological annotation. Regions of interest (ROIs) ( G-K ) were selected based on morphological and fluorescence staining for DNA (blue), CD3 (green), CD68/CD163 (red), and vimentin (yellow). ROIs bordering necrotic (G) granulomas and (H) solid or cellular granulomas were selected in addition to tertiary lymphoid structures (I), lymph node (J), and uninvolved lung (K) for spatial transcriptional profiling using the human whole <t>transcriptome</t> probe set using GeoMx (Bruker).
Geomx Digital Spatial Profiling (Dsp) Cancer Whole Transcriptome Atlas (Wta) System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial transcriptomics using GeoMx® DSP: slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) Representative haematoxylin and eosin (H&E) stained sections showing arterial lesions of varying severity (mild, moderate and severe). Specific regions are highlighted at a higher magnification to reveal morphological differences across lesion severity, indicating progressive changes from near normal to severe. ( B ) Workflow for spatial transcriptomics using GeoMx® DSP: slide preparation with morphology markers and ~18,000 oligo-conjugated RNA probes; selection of ROIs in each sample analysed; cleavage with UV light of barcodes from RNA probes; collection and release of collected barcodes onto a 96-well plate for all selected ROIs; generation of a cDNA library for next generation sequencing and upload of resulting sequencing data onto the GeoMx® DSP. ( C ) Fluorescent imaging of arterial lesions with varying severities, reflecting those shown at higher magnification in ( A ). Fluorescent imaging is a prerequisite for choosing regions of interest (ROIs) for downstream profiling by GeoMx. Samples were stained with SYTO13 (nuclear dye, blue), CD45 (pan-leucocyte marker, yellow) and CD4 (T cell subset marker, red). Representative ROIs chosen for downstream spatial profiling are indicated by white circles. .

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: Staining, Selection, cDNA Library Assay, Next-Generation Sequencing, Sequencing, Imaging, Marker

( A ) In situ expression of ANXA2 in a representative severe lesion in GeoMx® (top panel) and CosMx ™ (bottom panel). Higher magnification boxes show ANXA2 expression in an ATLO. Figure was reused to create this panel. ( B ) NanoString-provided workflow for spatial deconvolution of GeoMx® data. ( C ) Proposed workflow for spatial deconvolution utilising a CosMx-generated single cell matrix (from the same tissue) to inform cell estimates. .

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) In situ expression of ANXA2 in a representative severe lesion in GeoMx® (top panel) and CosMx ™ (bottom panel). Higher magnification boxes show ANXA2 expression in an ATLO. Figure was reused to create this panel. ( B ) NanoString-provided workflow for spatial deconvolution of GeoMx® data. ( C ) Proposed workflow for spatial deconvolution utilising a CosMx-generated single cell matrix (from the same tissue) to inform cell estimates. .

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: In Situ, Expressing, Generated

( A ) Heatmap of spatial deconvolution estimates using the inbuilt GeoMx® reference matrix 'safeTME'. Scaled abundances are shown as a ratio to the maximum value are displayed across five tissue localisations (adventitia, plaque, negative control, muscle and infiltrated muscle layer). 'Subsets' correspond to ROIs segmented on the GeoMx® platform and are highlighted. Cell types present in the safeTME matrix are indicated as rows. ( B ) Heatmap of the CosMx™-derived cell signature matrix. Census-annotated cell populations from the CosMx™ are represented as columns with rows representing genes on the CosMx™ platform. Genes are scaled from red to white, with red indicating a higher expression. ( C ) Heatmap of the genes present in the GeoMx® dataset from the CosMx™-derived cell signature matrix. ( D ) Heatmap of spatial deconvolution estimates using the CosMx™-derived matrix. Cell types present in the CosMx™-matrix are indicated as rows.

Journal: EMBO Molecular Medicine

Article Title: Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery

doi: 10.1038/s44321-025-00280-w

Figure Lengend Snippet: ( A ) Heatmap of spatial deconvolution estimates using the inbuilt GeoMx® reference matrix 'safeTME'. Scaled abundances are shown as a ratio to the maximum value are displayed across five tissue localisations (adventitia, plaque, negative control, muscle and infiltrated muscle layer). 'Subsets' correspond to ROIs segmented on the GeoMx® platform and are highlighted. Cell types present in the safeTME matrix are indicated as rows. ( B ) Heatmap of the CosMx™-derived cell signature matrix. Census-annotated cell populations from the CosMx™ are represented as columns with rows representing genes on the CosMx™ platform. Genes are scaled from red to white, with red indicating a higher expression. ( C ) Heatmap of the genes present in the GeoMx® dataset from the CosMx™-derived cell signature matrix. ( D ) Heatmap of spatial deconvolution estimates using the CosMx™-derived matrix. Cell types present in the CosMx™-matrix are indicated as rows.

Article Snippet: Spatial Transcriptomics GeoMx® DSP and CosMxTM SMI analyses of human coronary arteries with different stages of atherosclerosis progression provide state-of-the-art datasets to interrogate immune pathways involved in disease establishment and progression.

Techniques: Negative Control, Derivative Assay, Expressing

Representative H&E images of granulomas from A) Case 3, B) Case 2, and C) Case 4 showing a range of granuloma morphology with D) necrotizing granulomas, E) cellular non-necrotizing granulomas, and F) small, lymphocyte rich granulomas as assessed by a pulmonary pathologist using traditional morphological annotation. Regions of interest (ROIs) ( G-K ) were selected based on morphological and fluorescence staining for DNA (blue), CD3 (green), CD68/CD163 (red), and vimentin (yellow). ROIs bordering necrotic (G) granulomas and (H) solid or cellular granulomas were selected in addition to tertiary lymphoid structures (I), lymph node (J), and uninvolved lung (K) for spatial transcriptional profiling using the human whole transcriptome probe set using GeoMx (Bruker).

Journal: bioRxiv

Article Title: Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas

doi: 10.1101/2025.03.10.642376

Figure Lengend Snippet: Representative H&E images of granulomas from A) Case 3, B) Case 2, and C) Case 4 showing a range of granuloma morphology with D) necrotizing granulomas, E) cellular non-necrotizing granulomas, and F) small, lymphocyte rich granulomas as assessed by a pulmonary pathologist using traditional morphological annotation. Regions of interest (ROIs) ( G-K ) were selected based on morphological and fluorescence staining for DNA (blue), CD3 (green), CD68/CD163 (red), and vimentin (yellow). ROIs bordering necrotic (G) granulomas and (H) solid or cellular granulomas were selected in addition to tertiary lymphoid structures (I), lymph node (J), and uninvolved lung (K) for spatial transcriptional profiling using the human whole transcriptome probe set using GeoMx (Bruker).

Article Snippet: Due to the limited data on the functional role and significance of MDSCs in TB infected lung tissues, we used an unbiased spatial whole transcriptome analysis (WTA) platform (GeoMx, Bruker, Inc) integrated with single-cell immunophenotyping via highly multiplexed tissue cyclic immunofluorescence (CyCIF) to initiate this study of human TB.

Techniques: Fluorescence, Staining