geomx dsp instrument  (Spatial Transcriptomics Inc)

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: Neurobiology of disease

Article Title: Hepatic LRP-1 plays an important role in amyloidosis in Alzheimer’s disease mice: Potential role in chronic heavy alcohol feeding

doi: 10.1016/j.nbd.2024.106570

Figure Lengend Snippet: Representative histopathological images of the liver sections stained with hematoxylin-eosin to confirm steatosis in control- or ethanol-fed APP/PS1 mice ( A ). Scale bar = 200 μm. Significant downregulation of protein expression levels of LRP-1 in the livers of ethanol-fed APP/PS1 mice compared to control-fed APP/PS1 mice by Western blot analysis ( B) . Full-blot images are shown in . Significant positive correlations between the brain and liver TBS-soluble (Pearson r = 0.56, p < 0.05) ( C ) and insoluble (Pearson r = 0.73, p < 0.01) ( D ) mAβ42 levels. Representative images of the liver sections from the NanoString GeoMX DSP analyzer of the control- and ethanol-fed APP/PS1 mice showing sample regions of interest (ROIs: pericentral (circled yellow) and periportal (circled white)) selected for transcript analysis ( E ). Scale bar = 500 μm. Bar graphs showing a significant reduction in hepatic pericentral LRP-1 gene expression ( F ), and no significant change in the periportal LRP-1 gene expression ( G ) in the ethanol-fed APP/PS1 mice compared to the control-fed APP/PS1 mice. The data are expressed as Mean ± SEM of n = 7–9 per group and were analyzed using the unpaired t -test in B and LME with treatment as the fixed effect and mouse as the random effect in F and G, and individual ROIs analyzed per experimental group are shown in F and G. * p ≤ 0.05.

Article Snippet: The UV-photocleaved oligonucleotides collected from the ROIs were sequenced on an Illumina-Next-Generation Sequencing (NGS) instrument that results in spatially mapped digital counts, which were further uploaded onto the GeoMx DSP instrument for quality control check and data analysis.

Techniques: Staining, Control, Expressing, Western Blot, Gene Expression

Journal: bioRxiv

Article Title: GSK-3 inhibitor elraglusib enhances tumor-infiltrating immune cell activation in tumor biopsies and synergizes with anti-PD-L1 in a murine model of colorectal cancer

doi: 10.1101/2023.02.07.527499

Figure Lengend Snippet: Patient samples were analyzed using NanoString GeoMx Digital Spatial Profiling (DSP) technology. (A) Pie charts showing biopsy timepoint, primary tumor type, metastatic biopsy tissue type, and paired/unpaired biopsy sample information breakdowns. (B) A representative region of interest (ROI) showing PanCK+ and CD45+ masking. Green indicates CK, red indicates CD45, and blue indicates DAPI staining. (C) A Sankey diagram was used to visualize the study design where the width of a cord in the figure represents how many segments are in common between the two annotations they connect. The scale bar represents 50 segments. Blue cords represent CD45+ segments and yellow cords represent panCK+ segments. (D) Heatmap of all areas of interest (AOIs). Patient IDs, immune cell locations, biopsy timepoint, biopsy tissue, primary tumor location, and segment identity information are color coded as indicated in the legend. (E) PanCK+ ROI CD39 expression plotted against time-on-study (TOS). Points are color-coded by time on study (TOS) / time on treatment with darker blue points indicating a shorter TOS or time on treatment. (F) CD45+ ROI CD163 expression plotted against TOS. (G) Volcano plot showing a comparison of CD45+ region protein expression in post-treatment biopsies and pre-treatment biopsies regardless of timepoint. Grey points are non-significant (NS), blue points have p values < 0.05, and red points have false discovery rate (FDR) values less than 0.05. The size of the point represents the log2 UQ Signal-to-noise ratio (SNR). (H) Volcano plot showing a comparison of tumor-infiltrating CD45+ immune cell segment protein expression in pre- versus post-treatment biopsies. Grey points are nonsignificant (NS), blue points have p values < 0.05, and red points have false discovery rate (FDR) values less than 0.05. The size of the point represents the log2 UQ Signal-to-noise ratio (SNR).

Article Snippet: A NanoString GeoMx ® Digital Spatial Profiler (DSP) instrument (NanoString, Seattle, WA, USA) was used to scan slides, identify regions of interest (ROIs), and collect photocleavable barcodes according to manufacturer instructions.

Techniques: Staining, Expressing, Comparison