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

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

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