10x visium spatial transcriptomic spots  (Spatial Transcriptomics Inc)

Journal: bioRxiv

Article Title: Uncovering the Regional and Cell Specific Bioactivity of Injectable Extracellular Matrix Biomaterials in Myocardial Infarction through Spatial and Single Nucleus Transcriptomics

doi: 10.1101/2025.06.25.661525

Figure Lengend Snippet: (a) MI was induced followed by an intramyocardial injection of ECM hydrogel or saline 7 days post-MI. Hearts were then harvested for either snRNAseq or spatial transcriptomics 7 days post-injection (14 days post-MI). Sample size: n = 2 ECM hydrogel replicates, 7658 spots. (b) Myocardium (green) was labelled with anti-alpha-actinin antibody alongside fluorescently tagged ECM hydrogel (light blue). (c) The adjacent cryosection was used for spatial transcriptomics via 10X Visium, where the infarct containing ECM hydrogel (red) was found to cluster separately from the infarct alone (cyan). (d) The top upregulated differentially expressed genes defining the ECM hydrogel zone (red) were found to be immune and vascularly dominating genes compared to the down regulated genes impacting the infarct zone (cyan). (e-f) All differentially expressed genes in the ECM hydrogel zone (red) and infarct only zone were subjected to GO enrichment.

Article Snippet: Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide.

Techniques: Injection, Saline

Journal: bioRxiv

Article Title: Uncovering the Regional and Cell Specific Bioactivity of Injectable Extracellular Matrix Biomaterials in Myocardial Infarction through Spatial and Single Nucleus Transcriptomics

doi: 10.1101/2025.06.25.661525

Figure Lengend Snippet: (a) MI is induced followed by an intramyocardial injection of ECM hydrogel or saline 8 weeks post-MI. Hearts are then harvested for either snRNAseq or spatial transcriptomics 7 days post-injection. Sample size: n = 3 ECM hydrogel replicates, 9594 spots. (b) Myocardium (green) was labelled with an anti-alpha-actinin antibody alongside fluorescently tagged ECM hydrogel (light blue). (c) An adjacent cryosection to the immunofluorescence image in b was used for spatial transcriptomics via 10X Visium, where the infarct containing ECM hydrogel (red) was found to cluster separately from the normal infarct zone (cyan). (d) Top differentially expressed genes for both ECM within infarct (red) and infarct alone (cyan) are shown. (e-f) A comparison of the two zones reflects the ECM hydrogel activates fibroblasts and is responsible for further vascular development, as demonstrated through GO enrichment.

Article Snippet: Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide.

Techniques: Injection, Saline, Immunofluorescence, Comparison

Journal: bioRxiv

Article Title: Uncovering the Regional and Cell Specific Bioactivity of Injectable Extracellular Matrix Biomaterials in Myocardial Infarction through Spatial and Single Nucleus Transcriptomics

doi: 10.1101/2025.06.25.661525

Figure Lengend Snippet: (a) The top upregulated differentially expressed genes defining the ECM hydrogel zone (red) with integrated subacute and chronic Visium were found to be immune, fibroblast, and vascularly dominating genes compared to the downregulated genes impacting the infarct zone (cyan). Sample size: n = 2 for subacute ECM hydrogel (7658 spots); n = 3 for chronic ECM hydrogel (9594 spots) (b) The ECM zones in both subacute and chronic models of MI have higher expression of the matrix specific genes relative to the infarct zone. (c-f) Macrophages (c) , endothelial cells (d) , cardiomyocytes (e) , and fibroblasts (f) treated with ECM hydrogel in subacute and chronic MI were subsetted, reclustered and compared with respect to MI timepoint. Sample size: n = 2 subacute ECM hydrogel (downsampled to 3000 cells), n = 2 chronic ECM hydrogel (downsampled to 3000 cells). Top differentially expressed genes were displayed via Volcano Plot, and the differentially expressed genes were subjected to GO enrichment. (g) Comparison of transcriptomic findings between subacute and chronic MI.

Article Snippet: Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide.

Techniques: Expressing, Comparison

Journal: BMC Biology

Article Title: Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon

doi: 10.1186/s12915-025-02196-w

Figure Lengend Snippet: Wound healing in Atlantic salmon. a Histological micrographs depicting incisional wound at 2 days post-wounding (DPW), with Alcian blue and periodic acid-Schiff (PAS) staining to facilitate viewing of the incisional wound during the inflammation stage b Histological micrographs depicting incisional wound at 14 DPW, with Movat staining to facilitate viewing of the granulation tissue during the remodelling stage. c - f 10x Visium Spatial Transcriptomics Slides. Expression of putative pure MSC population 2 top 20 transcript from Seurat snRNA-seq data (Additional file 1: Table S10) at 2 DPW and 14 DPW ( c , d ). Expression of putative pure MSC population 1 top 20 transcripts from PHATE snRNA-seq analysis (Additional file 1: Table S10) at 2 DPW and 14 DPW ( e , f ). Wound bed (Wb), epidermis (Epi), dense connective tissue (Dct), skeletal muscle fibres (Mu), damaged white muscle fibres (Mu*), myosepta (Myo) and newly formed epithelial tissue (“Neo Epi”). Scales (Sc), adipose tissue (Adi), polymorphonucleated inflammatory cells (InF), granulation tissue (Gt), blood vessel formation (Bv) and fibril formation (Ff). Scale bars: 500 µm ( a – f ). The colour of the scale in c - f indicates the expression of transcripts mapped on the slide from low (blue) to high (red)

Article Snippet: Fig. 5 Wound healing in Atlantic salmon. a Histological micrographs depicting incisional wound at 2 days post-wounding (DPW), with Alcian blue and periodic acid-Schiff (PAS) staining to facilitate viewing of the incisional wound during the inflammation stage b Histological micrographs depicting incisional wound at 14 DPW, with Movat staining to facilitate viewing of the granulation tissue during the remodelling stage. c - f 10x Visium Spatial Transcriptomics Slides.

Techniques: Staining, Expressing

Journal: BMC Biology

Article Title: Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon

doi: 10.1186/s12915-025-02196-w

Figure Lengend Snippet: Charting the transcriptomic activity of different putative MSC-associated subclusters (10x Visium Spatial Transcriptomic slides). a-h Expression of MSC subtype-specific transcripts, taken from the Phate analysis (average expression of the top 20 markers of each subtype, Supplementary Table 11). Expression of bone precursors on day 2 and 14 DPW ( a , b ). Expression of adipocyte precursors on day 2 and 14 DPW ( c , d ). Expression of bone/muscle precursors on day 2 and 14 DPW ( e , f ). Expression of fibroblast 2 on day 2 and 14 DPW ( g , h ). Expression of fibroblast 3 on day 2 and 14 DPW ( i , j ). 2 DPW represents inflammation stage (right column) and 14 DPW represents remodelling stage (left column) of wound healing. Scale bars: 500 um ( a - j ). The colour of the scales in a-j indicates the expression of transcripts mapped to the slide from low (blue) to high (red)

Article Snippet: Fig. 5 Wound healing in Atlantic salmon. a Histological micrographs depicting incisional wound at 2 days post-wounding (DPW), with Alcian blue and periodic acid-Schiff (PAS) staining to facilitate viewing of the incisional wound during the inflammation stage b Histological micrographs depicting incisional wound at 14 DPW, with Movat staining to facilitate viewing of the granulation tissue during the remodelling stage. c - f 10x Visium Spatial Transcriptomics Slides.

Techniques: Activity Assay, Expressing