Journal: bioRxiv

Article Title: The U-method: Leveraging expression probability for robust biological marker detection

doi: 10.64898/2026.03.31.715470

Figure Lengend Snippet: (A) U-method analysis of scRNA-seq data from lung adenocarcinoma annotated by cell type. UMAP projection of all cell clusters and fibroblast and T-cell subclusters is shown (B) Feature plots showing the top U-markers of the main cell clusters shown in A. (C). Unscaled Dot plots of the top uniquely expressed genes per cluster. (D) Boxplots of U-score distributions across clusters and subclusters. (E) Projection of the average expression of identified markers onto a VisiumHD lung adenocarcinoma sample ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Article Snippet: We then projected the resulting UEG signatures (top 5 UEGs, U-score > 0.2) onto a publicly available lung adenocarcinoma Visium HD section ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Techniques: Expressing, Gene Expression

Journal: bioRxiv

Article Title: The U-method: Leveraging expression probability for robust biological marker detection

doi: 10.64898/2026.03.31.715470

Figure Lengend Snippet: (A) UMAP projections of scRNA-seq data from human colorectal cancer (CRC) and adjacent normal colon tissue split by sample origin, normal or tumor, analyzed by Seurat and annotated by major cell type. (B) Unscaled Dot plot of the top uniquely expressed genes per cluster. (C) Spatial maps showing the projection of uniquely expressed gene (UEG) signatures derived from scRNA-seq of epithelial and cancer cell clusters onto Visium HD CRC tissue sections. For each spot, signature values were computed as the raw average expression of U-method-identified marker genes associated with the epithelial or cancer cluster. No smoothing, normalization, or deconvolution were applied. Spots are plotted at their physical coordinates, with color intensity reflecting the signature value and transparency indicating detectable expression. Scale bar - 300 µm.

Article Snippet: We then projected the resulting UEG signatures (top 5 UEGs, U-score > 0.2) onto a publicly available lung adenocarcinoma Visium HD section ( https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt ).

Techniques: Derivative Assay, Expressing, Marker

Journal: Microbiology Spectrum

Article Title: A novel role of Dermatophagoides farinae -derived miR-276-3p in aggravating mite-induced allergic airway inflammation

doi: 10.1128/spectrum.01923-25

Figure Lengend Snippet: Dfa-miR-276-3p as a prime exacerbates DFE-induced airway inflammation in vivo . ( A ) Schematic diagram for construction of AAV-dfa-miR-276-3p-overexpressing mouse models. ( B ) Immunofluorescence assay detects co-expression of EGFP (green) and Claudin-1 (red) in mouse lung tissues, and the nuclei are stained with DAPI (blue) ( n = 3). Scale bar = 50 μm. ( C ) qPCR assay quantifies EGFP mRNA expression in mouse lung tissues. ( D ) qPCR assay quantifies dfa-miR-276-3p expression in mouse lung tissues. ( E ) Schematic diagram for construction of a mouse model of airway sensitization following AAV-dfa-miR-276-3p overexpression in lungs. ( F ) Total cell counts in mouse BALF ( n = 3). ( G ) ELISA measures IL-4 levels in mouse BALF ( n = 3). ( H ) ELISA measures IL-5 levels in mouse BALF ( n = 3). ( I ) ELISA measures IgE antibody levels in mouse serum samples ( n = 6). ( J ) ELISA measures IL-10 levels in mouse BALF ( n = 3). ( K ) HE and PAS staining of representative lung sections ( n = 3). Scale bar = 100 μm. ns, not significant, * P < 0.05, ** P < 0.01, and *** P < 0.001. Data are presented as means ± SEM. Difference of means among groups is tested for statistical significance with ANOVA, followed by Tukey’s post hoc test.

Article Snippet: Sections or cell culture slides were blocked with 10% goat serum at room temperature, and the cell culture slides were incubated with the primary anti-NF-κB p65 antibody (Cell Signaling Technology, Inc.), while the lung tissue sections were incubated with the primary anti-claudin 1 antibody (Proteintech, Manchester, UK).

Techniques: In Vivo, Immunofluorescence, Expressing, Staining, Over Expression, Enzyme-linked Immunosorbent Assay

Journal: Microbiology Spectrum

Article Title: A novel role of Dermatophagoides farinae -derived miR-276-3p in aggravating mite-induced allergic airway inflammation

doi: 10.1128/spectrum.01923-25

Figure Lengend Snippet: Dfa-miR-276-3p promotes DFE-induced airway inflammation through inhibiting STC1 expression to regulate ROS/NF-κB pathway in vivo . ( A ) Schematic diagram for different treatments of mice. ( B ) Total cell counts in mouse BALF ( n = 3). ( C ) ELISA measures IL-4 levels in mouse BALF ( n = 3). ( D ) ELISA measures IL-5 levels in mouse BALF ( n = 3). ( E ) ELISA measures IgE antibody levels in mouse serum samples ( n = 6). ( F ) ELISA measures IL-10 levels in mouse BALF ( n = 3). ( G ) HE and PAS staining of representative lung sections ( n = 3). Scale bar = 100 μm. ( H ) ROS levels in mouse lung tissues ( n = 6). ( I and J ) Western blotting determines STC1, NF-κB p65, and p-p65 protein expression in mouse lung tissues ( n = 3). ns, not significant, * P < 0.05, ** P < 0.01, and *** P < 0.001. Data are presented as means ± SEM. Difference of means among groups was tested for statistical significance with ANOVA, followed by Tukey’s post hoc test.

Article Snippet: Sections or cell culture slides were blocked with 10% goat serum at room temperature, and the cell culture slides were incubated with the primary anti-NF-κB p65 antibody (Cell Signaling Technology, Inc.), while the lung tissue sections were incubated with the primary anti-claudin 1 antibody (Proteintech, Manchester, UK).

Techniques: Expressing, In Vivo, Enzyme-linked Immunosorbent Assay, Staining, Western Blot