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

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

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