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bruker nanostring geomx immuno oncology panels  (Bruker Corporation)

 
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    Bruker Corporation bruker nanostring geomx immuno oncology panels
    <t>GeoMx</t> spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.
    Bruker Nanostring Geomx Immuno Oncology Panels, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/geomx/SKYSCAN+1272/pmc12402801-138-12-12
    Average 99 stars, based on 1 article reviews
    bruker nanostring geomx immuno oncology panels - by Bioz Stars, 2026-10
    99/100 stars

    Images

    1) Product Images from "SARC028 Samples Reveal an Interplay between TGF-β, IFN Signaling, and Low HLA Class I Expression as Contributors to Ewing Sarcoma Checkpoint Blockade Resistance"

    Article Title: SARC028 Samples Reveal an Interplay between TGF-β, IFN Signaling, and Low HLA Class I Expression as Contributors to Ewing Sarcoma Checkpoint Blockade Resistance

    Journal: Clinical Cancer Research

    doi: 10.1158/1078-0432.CCR-24-3882

    GeoMx spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.
    Figure Legend Snippet: GeoMx spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.

    Techniques Used: Expressing

    Related Articles

    Formalin-fixed Paraffin-Embedded:

    Article Title: Navigating the immunosuppressive brain tumor microenvironment using spatial biology
    Article Snippet: Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). .. Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). ..

    Multiplex Assay:

    Article Title: Navigating the immunosuppressive brain tumor microenvironment using spatial biology
    Article Snippet: Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). .. Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). ..

    Immunohistochemistry:

    Article Title: Navigating the immunosuppressive brain tumor microenvironment using spatial biology
    Article Snippet: Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). .. Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). ..

    RNAscope:

    Article Title: Navigating the immunosuppressive brain tumor microenvironment using spatial biology
    Article Snippet: Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). .. Currently, a range of platforms are available to assess the spatial transcriptome and proteome of FFPE tumor tissue including GeoMx and CosMx (Nanostring), Phenocycler (formally known as CODEX) and Opal multiplex IHC (Akoya Biosciences), RNAscope, MIBIscope, Merscope (Vizgen), Visium and Xenium (10x Genomics), SlideSeq and STOmics (BGI) [53–55] (Table 2). ..

    Gene Expression:

    Article Title: Breast cancer associated CD169 + macrophages possess broad immunosuppressive functions but enhance antibody secretion by activated B cells.
    Article Snippet: .. Proteome analysis of CD169+ macrophages in lymph nodes with breast tumor metastases using Nanostring GeoMX (Figure 3A) were compared to gene expression of the CD169+ (SIGLEC1) clusters in a public data set of Human breasts tumor single cell RNA Seq data from the Michigan Portal for the Analysis of NGS Data (MiPanda) (29) (Figure 3B). .. The primary breast cancer CD169+ TAMs were too few to analyse using the chosen Nanostring GeoMX proteome analysis method.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Single Cell:

    Article Title: Breast cancer associated CD169 + macrophages possess broad immunosuppressive functions but enhance antibody secretion by activated B cells.
    Article Snippet: .. Proteome analysis of CD169+ macrophages in lymph nodes with breast tumor metastases using Nanostring GeoMX (Figure 3A) were compared to gene expression of the CD169+ (SIGLEC1) clusters in a public data set of Human breasts tumor single cell RNA Seq data from the Michigan Portal for the Analysis of NGS Data (MiPanda) (29) (Figure 3B). .. The primary breast cancer CD169+ TAMs were too few to analyse using the chosen Nanostring GeoMX proteome analysis method.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    RNA Sequencing:

    Article Title: Breast cancer associated CD169 + macrophages possess broad immunosuppressive functions but enhance antibody secretion by activated B cells.
    Article Snippet: .. Proteome analysis of CD169+ macrophages in lymph nodes with breast tumor metastases using Nanostring GeoMX (Figure 3A) were compared to gene expression of the CD169+ (SIGLEC1) clusters in a public data set of Human breasts tumor single cell RNA Seq data from the Michigan Portal for the Analysis of NGS Data (MiPanda) (29) (Figure 3B). .. The primary breast cancer CD169+ TAMs were too few to analyse using the chosen Nanostring GeoMX proteome analysis method.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Next-Generation Sequencing:

    Article Title: Breast cancer associated CD169 + macrophages possess broad immunosuppressive functions but enhance antibody secretion by activated B cells.
    Article Snippet: .. Proteome analysis of CD169+ macrophages in lymph nodes with breast tumor metastases using Nanostring GeoMX (Figure 3A) were compared to gene expression of the CD169+ (SIGLEC1) clusters in a public data set of Human breasts tumor single cell RNA Seq data from the Michigan Portal for the Analysis of NGS Data (MiPanda) (29) (Figure 3B). .. The primary breast cancer CD169+ TAMs were too few to analyse using the chosen Nanostring GeoMX proteome analysis method.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Sequencing:

    Article Title: Leveraging spatial omics for the development of precision sarcoma treatments.
    Article Snippet: Spatial omics can perform cell phenotyping to study cell composition in the tissue, reveal the gene and molecular Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the secondmost prevalent solid cancer in children and adolescents.. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades.. Existing treatments are largely limited to chemotherapy, radiation, and surgery.

    Imaging:

    Article Title: Leveraging spatial omics for the development of precision sarcoma treatments.
    Article Snippet: Spatial omics can perform cell phenotyping to study cell composition in the tissue, reveal the gene and molecular Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the secondmost prevalent solid cancer in children and adolescents.. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades.. Existing treatments are largely limited to chemotherapy, radiation, and surgery.

    Fluorescence:

    Article Title: Leveraging spatial omics for the development of precision sarcoma treatments.
    Article Snippet: Spatial omics can perform cell phenotyping to study cell composition in the tissue, reveal the gene and molecular Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the secondmost prevalent solid cancer in children and adolescents.. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades.. Existing treatments are largely limited to chemotherapy, radiation, and surgery.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    In Situ Hybridization:

    Article Title: Leveraging spatial omics for the development of precision sarcoma treatments.
    Article Snippet: Spatial omics can perform cell phenotyping to study cell composition in the tissue, reveal the gene and molecular Sarcomas are rare and heterogeneous cancers that arise from bone or soft tissue, and are the secondmost prevalent solid cancer in children and adolescents.. Owing to the complex nature of pediatric sarcomas, the development of therapeutics for pediatric sarcoma has seen little progress in the past decades.. Existing treatments are largely limited to chemotherapy, radiation, and surgery.

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Staining:

    Article Title: GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery
    Article Snippet: .. Figure 5 Digital spatial protein immune profiling NanoString GeoMx of treatment-naive PDAC tumors and explorative analysis (A and B) Microscopical images illustrating immunofluorescent staining with morphological markers for PanCK (epithelial tumor cells), CD45 (immune cells), GATA6, and SYTO13 (DNA dye) in treatment-naive tumors. ..

    H&E Stain:

    Article Title: TIMP-1 is an activator of MHC-I expression in myeloid dendritic cells with implications for tumor immunogenicity
    Article Snippet: .. Hematoxylin & Eosin (H&E) staining was employed to identify and select tumor regions with immune cell infiltrates, guiding the precise selection of intersecting areas of tumor and immune cells for subsequent TMA construction and detailed spatial analysis by NanoString GeoMX. ..

    Immune Cell:

    Article Title: TIMP-1 is an activator of MHC-I expression in myeloid dendritic cells with implications for tumor immunogenicity
    Article Snippet: .. Hematoxylin & Eosin (H&E) staining was employed to identify and select tumor regions with immune cell infiltrates, guiding the precise selection of intersecting areas of tumor and immune cells for subsequent TMA construction and detailed spatial analysis by NanoString GeoMX. ..

    Selection:

    Article Title: TIMP-1 is an activator of MHC-I expression in myeloid dendritic cells with implications for tumor immunogenicity
    Article Snippet: .. Hematoxylin & Eosin (H&E) staining was employed to identify and select tumor regions with immune cell infiltrates, guiding the precise selection of intersecting areas of tumor and immune cells for subsequent TMA construction and detailed spatial analysis by NanoString GeoMX. ..

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Analysis:

    Article Title: TIMP-1 is an activator of MHC-I expression in myeloid dendritic cells with implications for tumor immunogenicity
    Article Snippet: .. Hematoxylin & Eosin (H&E) staining was employed to identify and select tumor regions with immune cell infiltrates, guiding the precise selection of intersecting areas of tumor and immune cells for subsequent TMA construction and detailed spatial analysis by NanoString GeoMX. ..

    Spatial Transcriptomics:

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    In Situ:

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    Transcriptomics:

    Article Title: Mapping the single cell spatial immune landscapes of the melanoma microenvironment
    Article Snippet: Multiplexed ion beam imaging (MIBI-TOF) , Time-of-flight Secondary Ion Mass Spectrometry , ~ 0.25 μm , Uses a beam of ions to image tissue and generate a mass spectrometry signal that can be used to image multiple targets at high resolution. , High spatial resolution, can analyze many targets simultaneously (up to 40 markers), allows rescanning of slides at multiple resolutions. , Requires specialized equipment and specialized expertise for analysis. , Taylor et al., 2021. [ ] . .. Spatial transcriptomics , RNA barcoding with UV-photocleavable linkers , 10 μm (for GeoMx), 50 nm (for CosMx) , Captures gene expression information in situ via RNA sequencing of tissue sections. Wide selection of assays including NanoString GeoMx (employing NGS-based Digital Spatial Profiling) and NanoString CosMx (employing Cyclic in-Situ Hybridization). , High-throughput, can provide information on gene expression patterns within tissues. , Limited to transcriptomics data, GeoMx provides high-throughput whole transcriptome information at the cellular-compartment level through fluorescence markers, does not provide information on protein localization. CosMx provides single-cell information on a more limited panel of RNA and proteins. , Hoefsmit et al., 2020; Thrane et al., 2018. [ , ] . .. Visium , Oligo capture probes , 55 μm , Molecular profiling of mRNA by spatially barcoded mRNA-binding oligonucleotides. , High-throughput and spatially resolved transcriptome data. , Limited resolution compared to other forms of spatial transcriptomics, analyzes ‘patches’ of 5–50 cells. , Quek et al., 2021. [ ] .

    other:

    Article Title: The HOPX and BLBP landscape and gliogenic regions in developing human brain
    Article Snippet: Furthermore, we tested applicability of high‐plex spatial profiling (Nanostring GeoMx ® ) on the same fetal specimens expanding the usage of this unique material.



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    geomx dsp  (Azenta)
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    Spatial transcriptomics workflow using <t>GeoMx</t> <t>DSP</t> 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .
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    geomx digital spatial profiling dsp  (Spatial Transcriptomics Inc)
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    Spatial Transcriptomics Inc geomx digital spatial profiling dsp
    Spatial transcriptomics workflow using <t>GeoMx</t> <t>DSP</t> 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .
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    geomx rna assay  (Spatial Transcriptomics Inc)
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    Spatial Transcriptomics Inc geomx rna assay
    Spatial transcriptomics workflow using <t>GeoMx</t> <t>DSP</t> 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .
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    geomx dsp ○ high plex spatial proteomics  (Spatial Transcriptomics Inc)
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    Spatial Transcriptomics Inc geomx dsp ○ high plex spatial proteomics
    Spatial transcriptomics workflow using <t>GeoMx</t> <t>DSP</t> 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .
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    geomx whole transcriptome atlas wta platform  (Spatial Transcriptomics Inc)
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    Spatial transcriptomics workflow using <t>GeoMx</t> <t>DSP</t> 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .
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    bruker nanostring geomx immuno oncology panels  (Bruker Corporation)
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    Bruker Corporation bruker nanostring geomx immuno oncology panels
    <t>GeoMx</t> spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.
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    Image Search Results


    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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .

    Journal: STAR Protocols

    Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues

    doi: 10.1016/j.xpro.2025.104282

    Figure Lengend Snippet: 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. Created in BioRender. G, M. (2025) https://BioRender.com/p7q0gem .

    Article Snippet: 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.

    Techniques: Hybridization, Staining, Imaging, Selection, Sequencing

    Representative images of GeoMx ROI selection on infected corneas Cross-sections of murine eyes at 24 h (left) and 48 h (right) post-infection. Fluorescent morphology markers visualize tissue architecture and immune cell infiltration (pink), guiding the placement of geometric Regions of Interest (ROIs, outlined in white) for spatial transcriptomic analysis.

    Journal: STAR Protocols

    Article Title: Protocol for dual spatial transcriptomic profiling of infected tissues

    doi: 10.1016/j.xpro.2025.104282

    Figure Lengend Snippet: Representative images of GeoMx ROI selection on infected corneas Cross-sections of murine eyes at 24 h (left) and 48 h (right) post-infection. Fluorescent morphology markers visualize tissue architecture and immune cell infiltration (pink), guiding the placement of geometric Regions of Interest (ROIs, outlined in white) for spatial transcriptomic analysis.

    Article Snippet: 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.

    Techniques: Selection, Infection

    GeoMx spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.

    Journal: Clinical Cancer Research

    Article Title: SARC028 Samples Reveal an Interplay between TGF-β, IFN Signaling, and Low HLA Class I Expression as Contributors to Ewing Sarcoma Checkpoint Blockade Resistance

    doi: 10.1158/1078-0432.CCR-24-3882

    Figure Lengend Snippet: GeoMx spatial proteomic analysis reveals changes in the stromal regions and full ROI from baseline to after treatment with pembrolizumab. A, The GeoMx analysis of specific cell types and regions. B, PCA of all the regions and masks collected by GeoMx. The stromal region and full ROI seem to have differences in the distribution of baseline and posttreatment samples. C, Heatmap showing protein expression profiles across the stromal mask from all patients. D, Significantly differentially expressed proteins between before and after treatment from the stromal region. Proteins associated with immune function (such as CD20, CD40, GITR, GZMA, and PD1) were lower in the stromal region following treatment. E, Heatmap showing protein expression profiles across the full ROI from all patients. F, Significantly differentially expressed proteins in the full ROI show an increase in immunoregulatory-related proteins between baseline and after treatment.

    Article Snippet: Specifically, we investigated the expression of 68 proteins contained in the combined Bruker/NanoString GeoMx immuno-oncology panels (Supplementary Table S1) on a slide consecutive to the one used for the multiplexed immunofluorescence (Vectra) analysis.

    Techniques: Expressing