Journal: Scientific Reports

Article Title: Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp

doi: 10.1038/s41598-024-61062-x

Figure Lengend Snippet: Heatmap of RNA-seq-based differential gene expression between wild-type (IT86D-101) and UCL homozygous mutant. UCL, unifoliate curled leaf; IT86D1_wildtype_bulk1, wild-type biological bulk replicate 1; IT86D2_wildtype_bulk2, wild-type biological bulk replicate 2; UCLHom1_mutant_bulk1, UCL homozygous mutant biological bulk replicate 1; UCLHom2_mutant_bulk2, UCL homozygous mutant biological bulk replicate 2.

Article Snippet: Strand-specific paired-end poly(A)-selected RNA-seq libraries of two bulked biological replicates, composed of 20 plants each of the purified RNA samples of UCLHom and IT86D-1010 were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

Techniques: RNA Sequencing Assay, Expressing, Mutagenesis

Journal: bioRxiv

Article Title: Log-linear scaling of TRPV4-KCNN4 transcripts tunes ROCK-dependent mechanotransduction in a DCIS progression model

doi: 10.64898/2026.02.19.706850

Figure Lengend Snippet: (A) TRPV4 mRNA expression across a six-line breast cancer progression panel. Isogenic MCF10A series (black circles) and patient-derived DCIS lines (gray circles) shown as log2 fold-change (FC) relative to MCF10DCIS.com. TRPV4 mRNA spans a >600-fold range (∼622-fold across the six-line panel). Log2FC values (cell line/MCF10DCIS.com): ETCC-06, −9.28; ETCC-10, −9.04; MCF10A, −7.27; MCF10AT1, −5.23; MCF10CA1a, −2.18; MCF10DCIS.com, 0. (B) Representative single-cell diffusivity ( D ) distributions under control (ctrl, blue), hyperosmotic stress (PEG300, Δ74.4 mOsm/L, gold), and pharmacologic TRPV4 inhibition (GSK2193874, 1 nM, green) conditions. Three cell lines represent negatively responsive (ETCC-06), non-responsive (MCF10A), and highly responsive (MCF10DCIS.com) phenotypes. Statistical significance determined by two-sided Mann-Whitney U test: ns, not significant; *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001. Each point is one cell; >100 cells total were tracked per condition across two independent experiments. (C–D) Motility indices (MI=< D _treatment>/) for hyperosmotic stress (MI_PEG, C ) and TRPV4 inhibition (MI_GSK219, D ) across all six cell lines. Mean±SD; >100 cells total were tracked per condition across two independent experiments. (E) Log-linear relationship between TRPV4 mRNA and MI_PEG (gold circles). Isogenic MCF10A series (solid gold line, n=4) shows robust correlation (R²=0.95, p=0.024). Extended panel including patient-derived lines (dashed gold line, n=6) maintains significance (R²=0.92, p=0.003). (F) Log-linear relationship between TRPV4 mRNA and MI_GSK219 (green circles). Isogenic series (solid green line, n=4) shows correlation (R²=0.91, p=0.048), validating the mRNA–output relationship with an orthogonal trigger. Extended panel (dashed green line, n=6): R²=0.89, p=0.005. (G) TRPV4 protein expression by Western blot. Cells cultured at normal density to match motility assay conditions. GAPDH: loading control. (H) Bulk TRPV4 protein abundance (from densitometry of the WB data) versus mechanotransduction output for both triggers. Dual y-axes show MI_PEG (gold, left) and MI_GSK219 (green, right) as functions of normalized TRPV4 protein expression. No significant correlation observed (n=6; MI_PEG vs protein: R²=0.09, p=0.57; MI_GSK219 vs protein: R²=0.12, p=0.50).

Article Snippet: RNA-seq library preparation and sequencing were performed by Azenta Life Sciences using a poly(A)-selected mRNA workflow.

Techniques: Expressing, Derivative Assay, Single Cell, Control, Inhibition, MANN-WHITNEY, Western Blot, Cell Culture, Motility Assay, Quantitative Proteomics

Journal: bioRxiv

Article Title: Log-linear scaling of TRPV4-KCNN4 transcripts tunes ROCK-dependent mechanotransduction in a DCIS progression model

doi: 10.64898/2026.02.19.706850

Figure Lengend Snippet: (A) Heatmap of candidate mechanotransduction genes across six cell lines ordered by increasing mechanotransduction capacity (ETCC-06 lowest to MCF10DCIS.com highest). Values are log2(mRNA_cell line/mRNA_MCF10DCIS.com). NA indicates log2 fold-change values that were not available from the differential-expression outputs used for fold-change extraction, resulting in gene-specific n<6 for some genes (e.g., PIEZO1/2). Superscripts indicate predominant localization: M, membrane; C, cytosolic; N, nuclear. (B) Summary correlations between candidate gene expression (log2FC vs MCF10DCIS.com) and mechanotransduction output (MI_PEG). Bars denote expression dynamic range across the panel; overlaid points report R² from linear regression of gene expression versus MI_PEG (red, p<0.05; orange, p≥0.05; purple, significant inverse correlation (p<0.05)). Among surveyed candidates, TRPV4 (R²=0.92, p=0.003) and KCNN4 (R²=0.94, p=0.002) show the strongest positive predictive relationships. (C) KCNN4 mRNA abundance predicts MI_PEG with log-linear scaling. Points represent individual cell lines; error bars: mean±SD. Dashed line: full panel regression (n=6, R²=0.94, p=0.002); solid line: isogenic MCF10A series (n=4, R²=0.81, p=0.099). (D) KCNN4 mRNA abundance predicts MI_GSK219 with similar log-linear scaling. Same plotting conventions as in (C) . Dashed line: full panel (n=6, R²=0.81, p=0.015); solid line: isogenic series (n=4, R²=0.67, p=0.184). (E) TRPV4 and KCNN4 mRNA levels are strongly correlated across the cell-line panel, indicating coordinated transcriptional regulation. Dashed line: full panel (n=6, R²=0.83, p=0.012); solid line: isogenic MCF10A series (n=4, R²=0.90, p=0.050). (F) Functional validation: pharmacologic KCNN4 inhibition (TRAM-34, 5 μM) phenocopies the motility increase induced by hyperosmotic stress (PEG300; Δ74.4 mOsm/L). Distributions show single-cell diffusion coefficients ( D ) for control, TRAM-34, PEG, and PEG+TRAM-34. TRAM-34 (0.094±0.120 µm²/s) and PEG (0.120±0.111 µm²/s) each increased motility versus control (0.054±0.088 µm²/s; both p<0.0001), with no additive effect in the combined condition (PEG+TRAM-34: 0.099±0.124 µm²/s, ns vs either alone). Each point is one cell; >100 cells total were tracked per condition across two independent experiments. Statistics: Mann-Whitney U test. **p<0.01; ****p<0.0001; ns, not significant.

Article Snippet: RNA-seq library preparation and sequencing were performed by Azenta Life Sciences using a poly(A)-selected mRNA workflow.

Techniques: Quantitative Proteomics, Extraction, Membrane, Gene Expression, Expressing, Functional Assay, Biomarker Discovery, Inhibition, Single Cell, Diffusion-based Assay, Control, MANN-WHITNEY