mouse single-cell rna-sequencing dataset  (GeneSearch Inc)

Journal: bioRxiv

Article Title: Self-Organizing Assembloids Reveal Enteric Nervous System Dynamics in Gut Homeostasis and Regeneration

doi: 10.1101/2025.01.14.632538

Figure Lengend Snippet: (a) Immunohistochemistry analysis of S100B (glia) and PDGFRA (mesenchymal cells) in healthy and damaged colon. Insets show the inclination of cells from the myenteric plexus to the submucosal plexus, indicated by arrowheads. (b) Whole-mount immunohistochemistry of colon tissue from healthy and damaged states, showing S100B (glia) and PDGFRA (mesenchymal cell) markers. (c) Histological analysis of TUJ1 (neuron) in healthy and damaged colon. Insets highlight the inclination of cells from the myenteric plexus to the submucosal plexus, with arrowheads showing the direction. (d) Violin plots of Ptn and Ptprz1 expression across different cell types, based on single-cell RNA sequencing data (Broad Institute Single Cell Portal Accession Number SCP1038). (e) Spatial transcriptomics analysis (GEO accession number GSE169749) of control and recovery animal models, showing Ptn and Ptprz1 expression. Each spot indicates expression levels, with higher expression in muscle regions. (f) qRT-PCR analysis of Ptn and Ptprz1 of control, no recovery, and 2-day recovery colon samples. Data are presented as mean ± SD with statistical analysis via ordinary one-way ANOVA and Tukey’s multiple comparisons (*p < 0.05, **p < 0.01, ****p < 0.0001). (g) Histological analysis of PTN, GFAP (glia), and PDGFRA in healthy and damaged colon. (h) Co-staining of PTPRZ1, GFAP (glia), and TUJ1 (neuron). At least three biological replicates (n=3) were used for qRT-PCR analysis, tissue and assembloid staining (three assembloids per experimental setup). Scale bar: 50 µm.

Article Snippet: The mouse single-cell RNA sequencing dataset utilized in this study is publicly available in the Broad Institute Single Cell Portal under the accession code SCP1038.

Techniques: Immunohistochemistry, Expressing, RNA Sequencing, Control, Quantitative RT-PCR, Staining

Journal: bioRxiv

Article Title: Self-Organizing Assembloids Reveal Enteric Nervous System Dynamics in Gut Homeostasis and Regeneration

doi: 10.1101/2025.01.14.632538

Figure Lengend Snippet: (a) Violin plots show expression of Ncam1, L1cam, Nrxn1 and Mcam in scRNA-seq data (Broad Institute Single Cell Portal Accession Number SCP1038). (b-e) Spatial transcriptomics analysis (GEO accession number GSE169749) of genes Ncam1, L1cam, Nrxn1, Mcam, Pdgfra and Pdgfa .

Article Snippet: The mouse single-cell RNA sequencing dataset utilized in this study is publicly available in the Broad Institute Single Cell Portal under the accession code SCP1038.

Techniques: Expressing

Journal: bioRxiv

Article Title: Self-Organizing Assembloids Reveal Enteric Nervous System Dynamics in Gut Homeostasis and Regeneration

doi: 10.1101/2025.01.14.632538

Figure Lengend Snippet: (a) Violin plots from the analysis of single-cell RNA sequencing data (Broad Institute Single Cell Portal Accession Number SCP1038) of healthy mouse colon show the expression patterns of Ptgs1, Ptgs2 , and Apoe . (b) qRT-PCR analysis of fat metabolism related genes. Change in gene expression levels of 15-PGDH, Acaa2, Apoe, Ptgs2, Pgd2s ; each point represents technical replicate of three biological replicates. Data presented as mean ± SD and analyzed with ordinary one way ANOVA with Tukey’s multiple comparisons test *p < 0.05, **p < 0.01, ****p < 0.0001. (c) Immunohistochemistry analysis of ACOT7, PDGFRA (mesenchymal cell) and HUC/D (neuron) in healthy colon. (d) Histological analysis of ACOT7, PDGFRA and E-CAD (epithelial cell) in healthy and damaged colon. At least 3 biological replicates (n=3) were used for tissue staining and qRT-PCR analysis. Scale bar: 50 µm.

Article Snippet: The mouse single-cell RNA sequencing dataset utilized in this study is publicly available in the Broad Institute Single Cell Portal under the accession code SCP1038.

Techniques: RNA Sequencing, Expressing, Quantitative RT-PCR, Gene Expression, Immunohistochemistry, Staining