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<t>Spatial</t> <t>transcriptomics</t> identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using <t>Seurat.</t> (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.
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<t>Spatial</t> <t>transcriptomics</t> identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using <t>Seurat.</t> (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.
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<t>Spatial</t> <t>transcriptomics</t> identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using <t>Seurat.</t> (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.
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r package seurat v4.05  (RStudio)
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<t>Spatial</t> <t>transcriptomics</t> identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using <t>Seurat.</t> (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.
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Spatial transcriptomics identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using Seurat. (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.

Journal: bioRxiv

Article Title: Vascular Patterning affects Intramembranous Ossification through HIF1α-Vegf Signaling

doi: 10.1101/2025.09.13.676037

Figure Lengend Snippet: Spatial transcriptomics identifies tissue based on gene expression patterns of 990 genes that comprise a whole-body panel on the NanoString CosMx platform. (A-C) Uniform Manifold Approximation and Projection (UMAP) clustering and a feature plot of the major tissue types in the mandibular region led to the identification of 14 cell populations: Mesenchyme 1 (0, blue), Masseter Muscle (1, red), Mesenchyme 2 (2, light green), Immature Osteoblasts (3, black), Endothelial Cells (4, dark pink), Tooth (5, dark green), Dental Mesenchyme (6, yellow), Meck el’s Cartilage (7, light blue), Myogenic Progenitors (8, brown), Glia (9, teal), Neurons (10, purple), Mature Osteoblasts (11, dark teal), Neuron (12, light pink), Epithelial cells (13, olive green), and Pericytes (14, dark red). Spatial transcriptomics-based expression of Col2a1 (purple, D-E) and Col1a1 (cyan, G-H) in the adjoining (AC) osteoblasts (black outlined) compared to non-adjoining (NAC) endothelial cells (pink outlined) in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Quantification of Col2a1 transcripts (F) and Col1a1 transcripts (I) were statistically analyzed using ANOVA. (J,K,N) Spatial transcriptomics-based expression of Aplnr (orange) in conjunction with Flt1 ( Vegfr1 , blue) and Pecam1 (green) around the mandible. (L,M) Vegfa (orange), Flt1 (blue) and Kdr ( Vegfr2 , green) expression was analyzed and used to generate figures in R using Seurat. (O) Quantification of the number of Vegfa positive cells in proximity to Vegfr1 positive cells compared to Vegfa positive cells in proximity to Vegfr2 positive cells in Med23 +/ECKO controls and Med23 ECKO/ECKO mutants. Statistical analysis was performed using ANOVA.

Article Snippet: Analysis of Spatial Transcriptomics was performed using Seurat Package (4.9.9.9041) in R (4.2.0).

Techniques: Gene Expression, Expressing