bulk rna sequencing data  (Novogene)

Journal: JID Innovations

Article Title: The human Flower isoform hFWE4 facilitates cornification in cutaneous squamous cell carcinoma

doi: 10.1016/j.xjidi.2026.100468

Figure Lengend Snippet: FWE KO dysregulates cornification and lamellar body–related gene expression in cSCC xenografts. ( a ) Volcano plot representing differential expression analysis of bulk RNA sequencing of hFWE WT (n = 12) and KO (n = 11) SCC-13 xenografts. Genes implicated in lamellar body function or cornification are annotated. ( b ) GO:BP and GO:CC analysis on differentially downregulated genes in hFWE- KO SCC-13 xenografts. ( c ) Representative immunofluorescence for KLK5 in hFWE WT and KO SCC-13 xenografts (bar = 500 μm and 50 μm [inset]). ( d ) Quantification of percentage tumor area KLK5 positive (mean ± SEM) in hFWE WT and KO SCC-13 xenografts (n = 6, 2-tailed unpaired t -test, ∗∗ P < .01). cSCC, cutaneous squamous cell carcinoma; GO:BP, gene ontology biological process; GO:CC; gene ontology cellular component; KO, knockout; WT, wild-type.

Article Snippet: Bulk RNA-sequencing data are available at the National Center for Biotechnology Information Gene Expression Omnibus under the accession number GSE314399 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE314399 ).

Techniques: Gene Expression, Quantitative Proteomics, RNA Sequencing, Immunofluorescence, Knock-Out

Journal: bioRxiv

Article Title: Characterization of effects of a neurotropic murine coronavirus infection on Alzheimer’s disease neuropathology of 5xFAD mice

doi: 10.64898/2026.02.23.707587

Figure Lengend Snippet: A) Experimental workflow for targeted 1000-plex single cell spatial transcriptomic imaging of 12 sagittal mouse brain sections (n=3/group). Fields of view (FOVs) was selected in dentate gyrus to represent the cell marker staining, segmentation, transcript counts, and cell typing based on transcript expression. DAPI, rRNA, Histone, and GFAP were used as cell markers. B) Uniform Manifold Approximation and Projection (UMAP) of 517,892 cells across all brain samples were captured with a mean transcript count of 841 transcripts per cell. Unbiased cell clustering at 1.0 resolution identified 42 clusters, which were manually annotated with a combination of automated and manual approaches with reference to Allen Brain Atlas single-cell RNA-seq cell types, gene expression, and anatomic location in XY space. C) 42 annotated clusters plotted in XY space with a representative JHMV-infected 5xFAD brain. D) Proportions of each major CNS cell type grouped by experimental group. E) Volcano plots of DEGs within each major CNS cell type across JHMV-infected 5xFAD vs. control 5xFAD. F) Differential downregulation (DD) and G) differential upregulation (DU) scores for JHMV-infected 5xFAD vs. control 5xFAD in each cluster plotted in XY space using a representative JHMV-infected 5xFAD brain. H) Pseudo-bulk expression of top DEGs in inhibitory neurons between JHMV-infected 5xFAD vs. control 5xFAD, grouped by experimental group. I) Inhibitory neurons in XY space in representative brain sections from each experimental group. J) Pathways enriched via Gene Ontology (GO) of downregulated DEGs in JHMV-infected 5xFAD vs. control.

Article Snippet: Read mapping analysis and statistics for bulk RNA sequencing data were performed by Novogene Co. Statistics for transcriptomic data (CosMx Spatial Molecular Imager) will be calculated using standard R packages, with a False Discovery Rate (FDR) <0.05.

Techniques: Single Cell, Imaging, Marker, Staining, Expressing, RNA Sequencing, Gene Expression, Infection, Control

Journal: Aging Cell

Article Title: Reduced Mitochondrial Adenine Nucleotide Translocase 1 ( ANT1 ) Correlates With Aging‐Associated Airway Remodeling

doi: 10.1111/acel.70264

Figure Lengend Snippet: SLC25A4 (ANT1) expression in human lungs is decreased in an age‐associated manner. (A–C) Single cell RNA sequencing from a healthy human dataset from the Human Lung Cell Atlas shows that SLC25A4 expression (log normalized, ln) decreases with age in the (A) airway basal cells ( r = −0.5151, p < 0.0001), (B) ciliated bronchial epithelial cells ( r = −0.3246, p < 0.0001), and (C) AT2 cells ( r = −0.1214, p < 0.0001). Tables in the data show the number of total cells analyzed (samples), number of human donors, number, and percentage of cells with expression of SLC25A4 (ANT1). Statistics for panels A–C by Pearson's r test with p ‐values in the legend. (D) Bulk RNA sequencing from the Tabula Muris database shows decreased Slc25a4 expression in female and male mice lungs over age. (E) Western blot and quantification relative to total protein intensity for Ant2 from mouse lungs of wildtype and Ant1 knockout (A1KO) mice, young and old ( n = 3–4 mice per group). * p < 0.05. Statistics by 2‐way ANOVA with Tukey's post‐test. Data are shown as mean ± SEM.

Article Snippet: Bulk RNA sequencing data from a mouse aging cell atlas database (Tabula Muris) showed decreased Slc25a4 expression in the lungs of female mice with increased age after 9 months old and a reduction in male mice after 18 months old (Figure ).

Techniques: Expressing, RNA Sequencing, Western Blot, Knock-Out

Journal: Aging Cell

Article Title: Reduced Mitochondrial Adenine Nucleotide Translocase 1 ( ANT1 ) Correlates With Aging‐Associated Airway Remodeling

doi: 10.1111/acel.70264

Figure Lengend Snippet: Loss of ANT1 resulted in dysregulation of collagen 8 in the airway epithelium with aging. (A) Bulk RNA sequencing was performed on human Beas‐2b cells with siRNA knockdown of ANT1 compared to non‐targeting control siRNA. Differential expression gene (DEG) analysis was performed and the top up and down‐regulated DEGs are shown with adjusted p < 0.05. (B) Key collagen genes that were upregulated or downregulated at a p < 0.05. (C) Western blot analysis of COL8A1 expression in Beas‐2b cells with Crispr‐Cas9 knockout of ANT1 compared to scrambled sgRNA control cells. Results were normalized to total protein intensity per lane. Statistics were calculated using unpaired Student's t ‐test. ** p < 0.001. (D) Immunofluorescence for Col8a1 in the CC10+ airway cells of mouse lung tissue sections. Col8a1 is shown in grayscale and composite with transmitted light brightfield, N = 4 for old WT and n = 3 for old A1KO. Data are shown as mean ± SEM. Statistics by Two‐way ANOVA with Tukey's post‐test. * p ‐value noted. (E) Immunofluorescence for COL8A1 in the ciliated cells (Acetyl‐α‐tubulin+) of the airways of healthy human lungs from young (31–45 years old, n = 6, 2 male and 4 females) versus aged subjects (73–76 years old, n = 6, 3 males and 3 females) separated by age range. Immunofluorescence data is reported as Integrated Density values from ImageJ. Data are shown as mean ± SEM. * p ‐value noted. Statistics were calculated using unpaired Student's t ‐test with Mann–Whitney post‐test.

Article Snippet: Bulk RNA sequencing data from a mouse aging cell atlas database (Tabula Muris) showed decreased Slc25a4 expression in the lungs of female mice with increased age after 9 months old and a reduction in male mice after 18 months old (Figure ).

Techniques: RNA Sequencing, Knockdown, Control, Quantitative Proteomics, Western Blot, Expressing, CRISPR, Knock-Out, Immunofluorescence, MANN-WHITNEY