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visium spatial transcriptomics sequencing  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc visium spatial transcriptomics sequencing
    Single‐cell and spatial transcriptome landscape of healthy and fibrotic kidneys after unilateral ischemia‐reperfusion injury (UIRI). a) Schematic representation of single‐cell RNA <t>sequencing</t> (scRNA‐seq) and spatial <t>transcriptomics</t> (ST) of kidneys from the sham and 10‐day UIRI mice, graphically designed with Biorender ( https://www.biorender.com/ ). b) t‐SNE plot illustrating the intricate cellular diversity in fibrotic kidneys, demonstrating distinct clusters representing glomerular endothelial cells (GEC), podocytes (Podo), mesangial cells (Mesa), Bowman's capsule epithelium (BC), proximal tubules (PT), descending limbs of Henle (DLOH), ascending limbs of Henle (ALOH), distal tubules (DT), principal cells (PC), intercalated cells (IC), fibroblasts (Fib), smooth muscle cells (SMC), extraglomerular endothelial cells (EGEC), monocytes (Mono), dendritic cells (DC), macrophages (Mϕ), plasmacytoid dendritic cells (pDC), proliferating mononuclear lineage (Prolif mono_L), and neutrophils (Neu), B cells (B), T cells (T), proliferating T cells (prolif T), and natural killer cells (NK). These cell types were further categorized into four major compartments: Glomerular, Renal, Interstitium, and Immune, as indicated by color grouping in the plot. c) Bubble plot illustrating the relative proportions of major kidney cell types in sham and UIRI samples. Each dot represents the proportion of a given cell type in a specific sample group, with dot size corresponding to its relative proportion. d) A comprehensive heatmap depicting the unique marker gene signature of major renal cell types. e) UMAP plot illustrating the inferred renal cell region distribution based on integrated spatial transcriptomics data from normal (Sham) and UIRI 10D mouse kidneys, generated using the 10x Genomics <t>Visium</t> platform. The identified regions include glomerular cells (Glom), distinct segments of the proximal tubule (PTS1, PTS1S2, PTS2), injured proximal tubules (InjPT), ascending limbs of Henle in cortex (ALOH(C)), distal tubules (DT), connecting tubules and collecting ducts (CNT_CD), cells at the corticomedullary junction (CMJ), fibrogenic niche regions (Niche1, Niche2), the inner stripe of the outer medulla (IOM), inner medulla (IM), renal capsule (RC), and perirenal tissue (Perirenal). f) Spatial maps illustrating the anatomical distribution of renal cell regions in Sham and UIRI 10D mouse kidneys. Region colors correspond to the classifications defined in panel (e). g) Bubble plot illustrating the relative proportions of major renal cell regions in spatial transcriptomics data from sham and UIRI 10D mouse kidneys. h) Bubble plot depicting the expression patterns of marker genes across distinct renal cell regions in spatial transcriptomics data. Dot color indicates the average gene expression level within each region, while dot size represents the proportion of spatial spots expressing the gene. i) Schematic diagram of nephron segmentation by cell types. j) Comparison of kidney anatomical regions and spatial transcriptomic clusters, showing clusters in kidney tissue (top) and the corresponding Visium H&E‐stained section (bottom). k) Renal tissue structure alterations at the corticomedullary junction (CMJ) in UIRI samples, showing the formation of two distinct fibrogenic niches, Niche1 and Niche2. l) A heatmap showing the deconvolution scores of cell type compositions across different regions in Visium spatial transcriptomics data, obtained using the RCTD method. m) Spatial FeaturePlots of RCTD‐derived cell type scores in the sham (top) and UIRI (bottom) groups, with paired panels sharing a common legend.
    Visium Spatial Transcriptomics Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/spatial+transcriptome+sequencing+visium+platform/sequencing+spatial+transcriptomics+visium/pmc12786295-261-6-7
    Average 86 stars, based on 1 article reviews
    visium spatial transcriptomics sequencing - by Bioz Stars, 2026-09
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    1) Product Images from "Single Cell and Spatial Transcriptomics Define a Proinflammatory and Profibrotic Niche After Kidney Injury"

    Article Title: Single Cell and Spatial Transcriptomics Define a Proinflammatory and Profibrotic Niche After Kidney Injury

    Journal: Advanced Science

    doi: 10.1002/advs.202503691

    Single‐cell and spatial transcriptome landscape of healthy and fibrotic kidneys after unilateral ischemia‐reperfusion injury (UIRI). a) Schematic representation of single‐cell RNA sequencing (scRNA‐seq) and spatial transcriptomics (ST) of kidneys from the sham and 10‐day UIRI mice, graphically designed with Biorender ( https://www.biorender.com/ ). b) t‐SNE plot illustrating the intricate cellular diversity in fibrotic kidneys, demonstrating distinct clusters representing glomerular endothelial cells (GEC), podocytes (Podo), mesangial cells (Mesa), Bowman's capsule epithelium (BC), proximal tubules (PT), descending limbs of Henle (DLOH), ascending limbs of Henle (ALOH), distal tubules (DT), principal cells (PC), intercalated cells (IC), fibroblasts (Fib), smooth muscle cells (SMC), extraglomerular endothelial cells (EGEC), monocytes (Mono), dendritic cells (DC), macrophages (Mϕ), plasmacytoid dendritic cells (pDC), proliferating mononuclear lineage (Prolif mono_L), and neutrophils (Neu), B cells (B), T cells (T), proliferating T cells (prolif T), and natural killer cells (NK). These cell types were further categorized into four major compartments: Glomerular, Renal, Interstitium, and Immune, as indicated by color grouping in the plot. c) Bubble plot illustrating the relative proportions of major kidney cell types in sham and UIRI samples. Each dot represents the proportion of a given cell type in a specific sample group, with dot size corresponding to its relative proportion. d) A comprehensive heatmap depicting the unique marker gene signature of major renal cell types. e) UMAP plot illustrating the inferred renal cell region distribution based on integrated spatial transcriptomics data from normal (Sham) and UIRI 10D mouse kidneys, generated using the 10x Genomics Visium platform. The identified regions include glomerular cells (Glom), distinct segments of the proximal tubule (PTS1, PTS1S2, PTS2), injured proximal tubules (InjPT), ascending limbs of Henle in cortex (ALOH(C)), distal tubules (DT), connecting tubules and collecting ducts (CNT_CD), cells at the corticomedullary junction (CMJ), fibrogenic niche regions (Niche1, Niche2), the inner stripe of the outer medulla (IOM), inner medulla (IM), renal capsule (RC), and perirenal tissue (Perirenal). f) Spatial maps illustrating the anatomical distribution of renal cell regions in Sham and UIRI 10D mouse kidneys. Region colors correspond to the classifications defined in panel (e). g) Bubble plot illustrating the relative proportions of major renal cell regions in spatial transcriptomics data from sham and UIRI 10D mouse kidneys. h) Bubble plot depicting the expression patterns of marker genes across distinct renal cell regions in spatial transcriptomics data. Dot color indicates the average gene expression level within each region, while dot size represents the proportion of spatial spots expressing the gene. i) Schematic diagram of nephron segmentation by cell types. j) Comparison of kidney anatomical regions and spatial transcriptomic clusters, showing clusters in kidney tissue (top) and the corresponding Visium H&E‐stained section (bottom). k) Renal tissue structure alterations at the corticomedullary junction (CMJ) in UIRI samples, showing the formation of two distinct fibrogenic niches, Niche1 and Niche2. l) A heatmap showing the deconvolution scores of cell type compositions across different regions in Visium spatial transcriptomics data, obtained using the RCTD method. m) Spatial FeaturePlots of RCTD‐derived cell type scores in the sham (top) and UIRI (bottom) groups, with paired panels sharing a common legend.
    Figure Legend Snippet: Single‐cell and spatial transcriptome landscape of healthy and fibrotic kidneys after unilateral ischemia‐reperfusion injury (UIRI). a) Schematic representation of single‐cell RNA sequencing (scRNA‐seq) and spatial transcriptomics (ST) of kidneys from the sham and 10‐day UIRI mice, graphically designed with Biorender ( https://www.biorender.com/ ). b) t‐SNE plot illustrating the intricate cellular diversity in fibrotic kidneys, demonstrating distinct clusters representing glomerular endothelial cells (GEC), podocytes (Podo), mesangial cells (Mesa), Bowman's capsule epithelium (BC), proximal tubules (PT), descending limbs of Henle (DLOH), ascending limbs of Henle (ALOH), distal tubules (DT), principal cells (PC), intercalated cells (IC), fibroblasts (Fib), smooth muscle cells (SMC), extraglomerular endothelial cells (EGEC), monocytes (Mono), dendritic cells (DC), macrophages (Mϕ), plasmacytoid dendritic cells (pDC), proliferating mononuclear lineage (Prolif mono_L), and neutrophils (Neu), B cells (B), T cells (T), proliferating T cells (prolif T), and natural killer cells (NK). These cell types were further categorized into four major compartments: Glomerular, Renal, Interstitium, and Immune, as indicated by color grouping in the plot. c) Bubble plot illustrating the relative proportions of major kidney cell types in sham and UIRI samples. Each dot represents the proportion of a given cell type in a specific sample group, with dot size corresponding to its relative proportion. d) A comprehensive heatmap depicting the unique marker gene signature of major renal cell types. e) UMAP plot illustrating the inferred renal cell region distribution based on integrated spatial transcriptomics data from normal (Sham) and UIRI 10D mouse kidneys, generated using the 10x Genomics Visium platform. The identified regions include glomerular cells (Glom), distinct segments of the proximal tubule (PTS1, PTS1S2, PTS2), injured proximal tubules (InjPT), ascending limbs of Henle in cortex (ALOH(C)), distal tubules (DT), connecting tubules and collecting ducts (CNT_CD), cells at the corticomedullary junction (CMJ), fibrogenic niche regions (Niche1, Niche2), the inner stripe of the outer medulla (IOM), inner medulla (IM), renal capsule (RC), and perirenal tissue (Perirenal). f) Spatial maps illustrating the anatomical distribution of renal cell regions in Sham and UIRI 10D mouse kidneys. Region colors correspond to the classifications defined in panel (e). g) Bubble plot illustrating the relative proportions of major renal cell regions in spatial transcriptomics data from sham and UIRI 10D mouse kidneys. h) Bubble plot depicting the expression patterns of marker genes across distinct renal cell regions in spatial transcriptomics data. Dot color indicates the average gene expression level within each region, while dot size represents the proportion of spatial spots expressing the gene. i) Schematic diagram of nephron segmentation by cell types. j) Comparison of kidney anatomical regions and spatial transcriptomic clusters, showing clusters in kidney tissue (top) and the corresponding Visium H&E‐stained section (bottom). k) Renal tissue structure alterations at the corticomedullary junction (CMJ) in UIRI samples, showing the formation of two distinct fibrogenic niches, Niche1 and Niche2. l) A heatmap showing the deconvolution scores of cell type compositions across different regions in Visium spatial transcriptomics data, obtained using the RCTD method. m) Spatial FeaturePlots of RCTD‐derived cell type scores in the sham (top) and UIRI (bottom) groups, with paired panels sharing a common legend.

    Techniques Used: RNA Sequencing, Marker, Generated, Expressing, Gene Expression, Comparison, Staining, Derivative Assay

    High‐resolution spatial transcriptomics and immunostaining reveal the TNC‐enriched fibroblast‐macrophage niche organization in fibrotic kidneys. a) Schematic diagram of the Visium HD workflow applied to kidney tissues from sham and UIRI model mice. b) UMAP visualization of integrated Visium HD spatial transcriptomics data from control mice (obtained from the 10x Genomics public dataset) and UIRI mice (this study), processed using canonical correlation analysis (CCA). This dimensionality reduction visualization reveals distinct clusters representing various renal parenchymal and stromal cell populations, including: Glomerulus, Vasculature, PTS1, PTS2, PTS1S2, InjPT, ascending limbs of Henle in cortex [ALOH(Cortex)], distal tubule and connecting tubule (DT_CNT), connecting tubule and collecting duct (CNT_CD), collecting duct in cortex [CD(Cortex)], PTS3, injured PTS3 (InjPTS3), Fibrogenic Niche, Vasa recta, loop of Henle in outer medulla [LOH(IOM)], collecting duct in outer medulla [CD(IOM)], collecting duct in inner medulla [CD(IM)], thin ascending limbs of Henle in inner medulla [tALOH(IM)], renal capsule (RC), Perirenal Fibrous tissue, and Perirenal Adipose tissue. c) Bubble plot comparing the regional distribution in Control versus UIRI 10d kidneys (Visium HD). d) Bubble plot depicting the expression patterns of marker genes across distinct renal cell regions in Visium HD data. e) Spatial maps generated using Visium HD illustrate the inferred anatomical distribution of renal cell regions in kidney tissues from Control and UIRI mice. f) Spatial Feature Plots of Visium HD data showing the spatial distribution of selected renal cell types in controls (top) and UIRI mice (bottom), based on cell‐type deconvolution using RCTD. g) A heatmap showing the correlation between NMF factors and cell‐type deconvolution scores in standard Visium spatial transcriptomics data. h) Spatial distribution of gene scores associated with the NMF factors most correlated with the fibrogenic niche, along with the contribution of key genes to each factor. i) Spatial FeaturePlots showing the anatomical distribution of Tnc expression in standard Visium. j) A heatmap showing the correlation between NMF factors and cell type deconvolution scores in Visium HD spatial transcriptomics data. k) Spatial distribution of NMF factors (NMF3 and NMF11) associated with the fibrogenic niche in Visium HD data, along with their corresponding high‐contributing genes. l) Spatial FeaturePlots showing the anatomical distribution of Tnc expression in Visium HD datasets. m) Immunofluorescence staining demonstrates colocalization of TNC with macrophages (F4/80⁺) in the CMJ interstitial region. From top to bottom: an overview merged image (Merge), followed by magnified views of TNC, Vimentin, and F4/80 staining in the same region, and an enlarged merged image (Enlarged Merge) at the bottom.
    Figure Legend Snippet: High‐resolution spatial transcriptomics and immunostaining reveal the TNC‐enriched fibroblast‐macrophage niche organization in fibrotic kidneys. a) Schematic diagram of the Visium HD workflow applied to kidney tissues from sham and UIRI model mice. b) UMAP visualization of integrated Visium HD spatial transcriptomics data from control mice (obtained from the 10x Genomics public dataset) and UIRI mice (this study), processed using canonical correlation analysis (CCA). This dimensionality reduction visualization reveals distinct clusters representing various renal parenchymal and stromal cell populations, including: Glomerulus, Vasculature, PTS1, PTS2, PTS1S2, InjPT, ascending limbs of Henle in cortex [ALOH(Cortex)], distal tubule and connecting tubule (DT_CNT), connecting tubule and collecting duct (CNT_CD), collecting duct in cortex [CD(Cortex)], PTS3, injured PTS3 (InjPTS3), Fibrogenic Niche, Vasa recta, loop of Henle in outer medulla [LOH(IOM)], collecting duct in outer medulla [CD(IOM)], collecting duct in inner medulla [CD(IM)], thin ascending limbs of Henle in inner medulla [tALOH(IM)], renal capsule (RC), Perirenal Fibrous tissue, and Perirenal Adipose tissue. c) Bubble plot comparing the regional distribution in Control versus UIRI 10d kidneys (Visium HD). d) Bubble plot depicting the expression patterns of marker genes across distinct renal cell regions in Visium HD data. e) Spatial maps generated using Visium HD illustrate the inferred anatomical distribution of renal cell regions in kidney tissues from Control and UIRI mice. f) Spatial Feature Plots of Visium HD data showing the spatial distribution of selected renal cell types in controls (top) and UIRI mice (bottom), based on cell‐type deconvolution using RCTD. g) A heatmap showing the correlation between NMF factors and cell‐type deconvolution scores in standard Visium spatial transcriptomics data. h) Spatial distribution of gene scores associated with the NMF factors most correlated with the fibrogenic niche, along with the contribution of key genes to each factor. i) Spatial FeaturePlots showing the anatomical distribution of Tnc expression in standard Visium. j) A heatmap showing the correlation between NMF factors and cell type deconvolution scores in Visium HD spatial transcriptomics data. k) Spatial distribution of NMF factors (NMF3 and NMF11) associated with the fibrogenic niche in Visium HD data, along with their corresponding high‐contributing genes. l) Spatial FeaturePlots showing the anatomical distribution of Tnc expression in Visium HD datasets. m) Immunofluorescence staining demonstrates colocalization of TNC with macrophages (F4/80⁺) in the CMJ interstitial region. From top to bottom: an overview merged image (Merge), followed by magnified views of TNC, Vimentin, and F4/80 staining in the same region, and an enlarged merged image (Enlarged Merge) at the bottom.

    Techniques Used: Immunostaining, Control, Expressing, Marker, Generated, Immunofluorescence, Staining

    TLR4 knockout in macrophages attenuates renal inflammation and renal fibrosis in vivo. a) The diagram shows the experimental protocol. Bone marrow chimera models were established by transplanting the WT bone marrow to WT mice, or TLR4 KO bone marrow to WT mice. Mice were irradiated at a single dose of 1100 Rads and then underwent bone marrow transplantation. After 8 weeks of successful transplantation, a unilateral ischemia‐reperfusion (UIRI) model was established. b) PCR‐based identification of kidney genotypes in the recipient mice of bone marrow transplantation models using TLR4 mutation site primers and wild‐type site primers, respectively. c,d) Graphic presentations show serum creatinine (Scr) (c) and blood urea nitrogen (BUN) (d) levels in different groups as indicated at 11 days after IRI. * p < 0.05 versus WT‐WT (n = 4–6). e,f) Western blot analyses show renal expression of TLR4, p‐P65, and P65 in different groups as indicated. Representative Western blot (e) and quantitative data (f) are shown. * p < 0.05 versus WT‐WT (n = 4–6). g) Representative micrographs show renal expression and co‐localization of TLR4 and F4/80 by immunofluorescence staining in different groups as indicated. The areas between the dashed lines represent the corticomedullary junction of the kidney. h,i) Western blot analyses show renal expression of MR, Arg‐1, iNOS, TNF‐α, and CCL2 in different groups as indicated. Representative Western blot (h) and quantitative data (i) are shown. * p < 0.05 versus WT‐WT (n = 4–6). j,k) Western blot analyses show renal expression of TNC, FN, and α‐SMA in different groups as indicated. Representative Western blot (j) and quantitative data (k) are shown. * p < 0.05 versus WT‐WT (n = 4–6). l) A schematic diagram shows a crucial role of TNC in organizing the proinflammatory and profibrotic niche. By integrating single‐cell RNA sequencing and spatial transcriptomics, we unveil TNC as a central organizer of the proinflammatory and profibrotic niche in kidney fibrosis. TNC promotes macrophage activation through TLR4/NF‐κB signaling, leading to macrophage activation, proliferation, and cytokine production.
    Figure Legend Snippet: TLR4 knockout in macrophages attenuates renal inflammation and renal fibrosis in vivo. a) The diagram shows the experimental protocol. Bone marrow chimera models were established by transplanting the WT bone marrow to WT mice, or TLR4 KO bone marrow to WT mice. Mice were irradiated at a single dose of 1100 Rads and then underwent bone marrow transplantation. After 8 weeks of successful transplantation, a unilateral ischemia‐reperfusion (UIRI) model was established. b) PCR‐based identification of kidney genotypes in the recipient mice of bone marrow transplantation models using TLR4 mutation site primers and wild‐type site primers, respectively. c,d) Graphic presentations show serum creatinine (Scr) (c) and blood urea nitrogen (BUN) (d) levels in different groups as indicated at 11 days after IRI. * p < 0.05 versus WT‐WT (n = 4–6). e,f) Western blot analyses show renal expression of TLR4, p‐P65, and P65 in different groups as indicated. Representative Western blot (e) and quantitative data (f) are shown. * p < 0.05 versus WT‐WT (n = 4–6). g) Representative micrographs show renal expression and co‐localization of TLR4 and F4/80 by immunofluorescence staining in different groups as indicated. The areas between the dashed lines represent the corticomedullary junction of the kidney. h,i) Western blot analyses show renal expression of MR, Arg‐1, iNOS, TNF‐α, and CCL2 in different groups as indicated. Representative Western blot (h) and quantitative data (i) are shown. * p < 0.05 versus WT‐WT (n = 4–6). j,k) Western blot analyses show renal expression of TNC, FN, and α‐SMA in different groups as indicated. Representative Western blot (j) and quantitative data (k) are shown. * p < 0.05 versus WT‐WT (n = 4–6). l) A schematic diagram shows a crucial role of TNC in organizing the proinflammatory and profibrotic niche. By integrating single‐cell RNA sequencing and spatial transcriptomics, we unveil TNC as a central organizer of the proinflammatory and profibrotic niche in kidney fibrosis. TNC promotes macrophage activation through TLR4/NF‐κB signaling, leading to macrophage activation, proliferation, and cytokine production.

    Techniques Used: Knock-Out, In Vivo, Irradiation, Transplantation Assay, Mutagenesis, Western Blot, Expressing, Immunofluorescence, Staining, RNA Sequencing, Activation Assay

    Related Articles

    Spatial Transcriptomics:

    Article Title: Single Cell and Spatial Transcriptomics Define a Proinflammatory and Profibrotic Niche After Kidney Injury
    Article Snippet: .. For the preparation of sections for Visium Spatial Transcriptomics sequencing, samples were equilibrated at −18 °C and a 10 μm thick section was cut onto the active sequencing area (6 mm x 6 mm) of a spatial barcoded slide. ..

    Sequencing:

    Article Title: Single Cell and Spatial Transcriptomics Define a Proinflammatory and Profibrotic Niche After Kidney Injury
    Article Snippet: .. For the preparation of sections for Visium Spatial Transcriptomics sequencing, samples were equilibrated at −18 °C and a 10 μm thick section was cut onto the active sequencing area (6 mm x 6 mm) of a spatial barcoded slide. ..



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    (A) Experimental workflow for, and analysis of, single-cell <t>transcriptome</t> (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.
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    Image Search Results


    (A) Experimental workflow for, and analysis of, single-cell transcriptome (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.

    Journal: bioRxiv

    Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

    doi: 10.1101/2023.08.18.553804

    Figure Lengend Snippet: (A) Experimental workflow for, and analysis of, single-cell transcriptome (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.

    Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

    Techniques: In Situ, Translocation Assay, Gene Expression, Labeling, In Situ Hybridization, Marker

    (A) ScRNA/ST-seq and meta-transcriptome data show an intimate interaction of sterol metabolism between the host and symbionts. In support of this, immunofluorescence (IF) assay (using gills of the InS group) of the 24-hydroxycholesterol 7 alpha-hydroxylase (CYP39A1) protein shows that CYP39A1 proteins are widely distributed across bacteriocytes. In addition, a more intensive signal of CYP39A1 protein could also be observed at the apical region that enriched with endosymbionts (indicated by lipid A signals). (B) ScRNA/ST-seq and meta-transcriptome data show intimate interaction of glucose/glycogen metabolism between the host and symbionts. In support of this, IF assay of the sugar phosphate exchanger (SLC37A2) protein shows the co-location of SLC37A2 proteins with endosymbionts inside bacteriocytes. (C) ScRNA/ST-seq and meta-transcriptome data show intimate interactions of ammonia metabolism between the host and symbionts. In support of this, IF assay of the ammonium transporter Rh (RHBG-A) protein shows co-location of RHBG-A proteins with endosymbionts inside bacteriocytes.

    Journal: bioRxiv

    Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

    doi: 10.1101/2023.08.18.553804

    Figure Lengend Snippet: (A) ScRNA/ST-seq and meta-transcriptome data show an intimate interaction of sterol metabolism between the host and symbionts. In support of this, immunofluorescence (IF) assay (using gills of the InS group) of the 24-hydroxycholesterol 7 alpha-hydroxylase (CYP39A1) protein shows that CYP39A1 proteins are widely distributed across bacteriocytes. In addition, a more intensive signal of CYP39A1 protein could also be observed at the apical region that enriched with endosymbionts (indicated by lipid A signals). (B) ScRNA/ST-seq and meta-transcriptome data show intimate interaction of glucose/glycogen metabolism between the host and symbionts. In support of this, IF assay of the sugar phosphate exchanger (SLC37A2) protein shows the co-location of SLC37A2 proteins with endosymbionts inside bacteriocytes. (C) ScRNA/ST-seq and meta-transcriptome data show intimate interactions of ammonia metabolism between the host and symbionts. In support of this, IF assay of the ammonium transporter Rh (RHBG-A) protein shows co-location of RHBG-A proteins with endosymbionts inside bacteriocytes.

    Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

    Techniques: Immunofluorescence