Journal: Cells

Article Title: Transcriptomic Analysis of Adult Mouse Cardiac Stromal Cells Using Single-Cell qRT-PCR

doi: 10.3390/cells15040384

Figure Lengend Snippet: Single-cell analysis reveals enrichment of Tcf21 and low expression of Tbx5 in CTs compared to CDCs and CFs. ( A ) Expression of 43 genes was analysed at the single-cell level in the four cell populations shown: CTs ( n = 55), CDCs ( n = 41), and CFs ( n = 29) at passage 3, as well as HL-1 cardiomyocytes ( n = 13). Both CTs and CDCs represent 3 biological replicates. The heatmap illustrates expression as −∆CT values (blue indicates low or absent expression; red indicates high expression). Samples were ordered based on cell type, and the genes were grouped using a hierarchical clustering algorithm based on the underlying co-expression pattern. ( B ) Single-cell expression of the 43 genes tested, shown individually for the four cell populations, with the mean represented as a black diamond in each group.

Article Snippet: Tbx5 , Mm00803518_m1 , Ddr2 , Mm00445615_m1.

Techniques: Single-cell Analysis, Expressing, Single Cell

Journal: Cells

Article Title: Transcriptomic Analysis of Adult Mouse Cardiac Stromal Cells Using Single-Cell qRT-PCR

doi: 10.3390/cells15040384

Figure Lengend Snippet: PCA of the three cardiac stromal populations and HL-1 cardiomyocytes. ( A ) PCA of the four cell populations shown: CTs ( n = 55), CDCs ( n = 41), and CFs ( n = 29) at passage 3, as well as HL-1 cardiomyocytes ( n = 13). Both CTs and CDCs represent 3 biological replicates. Dim.1 separates the cardiac stromal populations, whereas Dim.2 shows a distinct separation between cardiac stromal and myocyte populations. Gene loadings contributing to each Dim suggest that a small subset of genes explains the cross-group variability captured by Dim.1 and Dim.2. Tcf21 is associated with CTs (emphasised by the blue circle), whereas Tbx5 is associated with CDCs and CFs (emphasised by the brown circle). The separation between cardiac stromal and myocyte populations is reflected by clustering of core cardiac and cardiomyocyte genes ( Nkx2-5 , Wif1 , Nppa , Myl2 , and Myh6 ), which are emphasised by the pink circle. ( B ) PCA of the three cardiac stromal populations alone: CTs ( n = 28), CDCs ( n = 41), and CFs ( n = 27). Both CTs and CDCs represent 3 biological replicates. Gene loadings contributing to each Dim show that Tcf21 is associated with CTs, whereas Tbx5 is associated with CDCs and CFs.

Article Snippet: Tbx5 , Mm00803518_m1 , Ddr2 , Mm00445615_m1.

Techniques:

Journal: iScience

Article Title: Hyperlipidemia exacerbates frozen shoulder fibrosis by activating the TGF-β/Smad2/3 signaling pathway via the TBX5-TNC-Itgα2 axis

doi: 10.1016/j.isci.2026.114660

Figure Lengend Snippet: Transcriptomic analysis and histological validation of shoulder joint capsule tissue in hyperlipidemic rats (A) Heatmap displaying differentially expressed genes in shoulder joint capsule tissue of normal control (NC) and hyperlipidemic (HL) rats. (B) Volcano plot showing the distribution of differentially expressed genes in shoulder joint capsule tissue of HL rats compared to NC rats. (C) Bar graph illustrating the top 30 enriched gene ontology (GO) terms for differentially expressed genes in shoulder joint capsule tissue of HL rats. (D) Bar graph illustrating the top 30 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for differentially expressed genes in shoulder joint capsule tissue of HL rats. (E) Protein-protein interaction (PPI) network of differentially expressed genes in shoulder joint capsule tissue of HL rats. (F) Prediction of potential TNC transcription factors. (G) Dual-luciferase reporter assay results examining the effect of TBX5 overexpression on the transcriptional activity of wild-type (WT) and mutant (MUT) TNC promoters. ∗∗ p < 0.01(vs. pcDNA3.1-NC + pGL4.11-TNC-3′UTR-WT), ## p < 0.01(vs. pcDNA3.1-TBX5 + pGL4.11-TNC-3′UTR-WT). (H) Chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) experiment validating the direct binding of the TBX5 protein to specific regions of the TNC promoter. (I) Representative images of hematoxylin and eosin (H&E) stained shoulder joint capsule tissue sections from NC and HL rats. (J) Representative images of Masson’s trichrome stained shoulder joint capsule tissue sections from NC and HL rats. (K) Quantitative real-time PCR (qPCR) analysis of mRNA expression levels of selected genes in shoulder joint tissue of NC and HL rats. (L) Western blot analysis of protein expression levels of selected proteins in shoulder joint tissue of NC and HL rats. n = 3 biologically independent rats per group for transcriptomic analysis (A–E). n = 3 biologically independent experiments (G–H). n = 6 biologically independent rats per group (I–L). Data are represented as mean ± SD. Statistical analyses were performed using Student’s t tests for two groups (H, K, and L) and one-way ANOVA followed by Tukey’s post hoc test for multiple comparisons (G). ∗ p < 0.05, ∗∗ p < 0.01 and ∗∗∗ p < 0.001.

Article Snippet: pcDNA3.1-TBX5 , Shanghai Genechem Co.,Ltd. , N/A.

Techniques: Biomarker Discovery, Control, Luciferase, Reporter Assay, Over Expression, Activity Assay, Mutagenesis, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, ChIP-qPCR, Binding Assay, Staining, Expressing, Western Blot

Journal: bioRxiv

Article Title: Developmental and transcriptional programs that define the initiation of the forelimb

doi: 10.1101/2025.11.23.689776

Figure Lengend Snippet: ( A-R ) Cryosections showing expression of the indicated markers at 10 somites (left column), 13 somites (middle column) and 15 somites (right column). Arrows point to the apical side of the somatic LPM. ( A-F ) N-Cadherin expression. ( G-I ) β-Catenin expression. ( J-O ) Dual immunofluorescence and HCR fluorescent in situ hybridization showing co-expression of aPKC and Tbx5 gene expression. Note the low levels of aPKC staining and lack of polarized expression in the forelimb field and ( P-R ) LAMININ expression.

Article Snippet: Approximately 50 μg of chromatin was sheared using a Diagenode Bioruptor-300 before incubating overnight with a TBX5 polyclonal antibody (R&D Systems #AF5918).

Techniques: Expressing, Immunofluorescence, In Situ Hybridization, Gene Expression, Staining

Journal: bioRxiv

Article Title: Developmental and transcriptional programs that define the initiation of the forelimb

doi: 10.1101/2025.11.23.689776

Figure Lengend Snippet: (A) Schematic of the experiment showing the dissected region of the embryo used to perform paired RNA-Seq and Ribosome profiling. (B) Length distribution of ribosome protected footprints for the 10 and 14 somite stages, shaded area shows deviation between biological triplicates. (C) Mapping of ribosome profiling reads to different transcript features (CDS, 5′ UTR, and 3′ UTR) is presented for each stage. Error bars indicate the standard deviation. (D) Metagene plots for ribosome occupancy around the translational start (top) and stop (bottom). Note that the 5’ ends of mapped reads are plotted hence the characteristic offset relative to the start and stop site are observed. (E) Pairwise correlation matrix of the generated RNA-Seq and ribosome occupancy libraries. Boxes are color coded with darker shades representing higher Spearman’s correlation coefficient. (F) RNA expression and ribosome occupancy of limb bud specifier genes ( Fgf10, Tbx5 ), genes not detected in limb bud ( Fgf8, Shh ) and cell polarity and EMT related genes: aPKC ( Prkci), N-Cadherin (Cdh2), Vimentin (Vim), β-catenin (Ctnnb1) , Twist (Twist1) , Snail (Snai1) and Slug (Snai2) at 10 and 14 somite stages. RPKM values (y-axis) for each biological replicate are shown in circles with the mean depicted with a horizontal line.

Article Snippet: Approximately 50 μg of chromatin was sheared using a Diagenode Bioruptor-300 before incubating overnight with a TBX5 polyclonal antibody (R&D Systems #AF5918).

Techniques: RNA Sequencing, Standard Deviation, Generated, RNA Expression

Journal: bioRxiv

Article Title: Developmental and transcriptional programs that define the initiation of the forelimb

doi: 10.1101/2025.11.23.689776

Figure Lengend Snippet: (A) Precision recall plot for the random forest predictions using the top 10 marker genes in predicting somatic LPM cells. Marker genes alone (orange) or in combination with Tbx5 (blue) and probability of random prediction (Baseline) and all top10 genes together (cyan) are shown. Precision is the proportion of number of times the prediction was correct and recall is the proportion of somatic LPM cells that were correctly predicted by the gene. (B) Overlaid HCR image showing the expression of Tbx5 , Unc5c , Plxn4a and Tbx5 , Sema3a , Scube1 in 15-16 somite whole mouse embryos, (C) Correlation plots showing the expression of Tbx5 with the experimentally validated marker genes ( Unc5c , Plxna4 , Sema3a and Scube1 ). 1000 random cells are plotted for effective visualization. Log-normalized expression values are plotted on both the x-axis and y-axis. (D-G) Zoomed images of the developing limb field in 15-16 somite embryos. The images on the far right depict volumetric renderings showing the overlap between the Tbx5 expression domain and that of the indicated gene in the forelimb field (H) Quantification of the overlap between the Tbx5 domain and the indicated genes. (D-H) n=4 biological replicates for Sema3a and Scube1 and n=5 for Unc5c and Plxna4 .

Article Snippet: Approximately 50 μg of chromatin was sheared using a Diagenode Bioruptor-300 before incubating overnight with a TBX5 polyclonal antibody (R&D Systems #AF5918).

Techniques: Marker, Expressing

Journal: bioRxiv

Article Title: Developmental and transcriptional programs that define the initiation of the forelimb

doi: 10.1101/2025.11.23.689776

Figure Lengend Snippet: (A) The TBX5 signature target gene set is significantly enriched for cell adhesion and neuron projection development GO terms (terms indicate the adjusted p-value and number of enriched genes. (B) Vein diagram showing intersection between all genes with TBX5 binding regions and somatic LPM signature genes identified by ChIP sequencing for TBX5 from E10.5 stage embryos. (C) The expected versus observed number of genes with TBX5 binding sites. The number of TBX5-associated genes observed in the Somatic Lateral Plate Mesoderm group (26/30) was compared to a null distribution generated from 10,000 random draws of 30 genes. (D) Box plot showing the number of TBX5 binding regions per gene for somatic LPM signature genes and all other genes. (E-H) Coverage plots showing TBX5 ChIP-seq reads across Fgf10 , Sema3a , Plxna4 and Unc5c genomic regions respectively. (I) Graphical illustration of the phenotypic and gene expression changes happening in the somatic LPM from 10-18 somites.

Article Snippet: Approximately 50 μg of chromatin was sheared using a Diagenode Bioruptor-300 before incubating overnight with a TBX5 polyclonal antibody (R&D Systems #AF5918).

Techniques: Binding Assay, ChIP-sequencing, Generated, Gene Expression