clone: 1a8 nb253131afd antibody  (Novus Biologicals)

Journal: Cell Genomics

Article Title: Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors

doi: 10.1016/j.xgen.2025.100805

Figure Lengend Snippet: Non-biased whole-mouse transcriptome analysis of P. aeruginosa -infected tissues reveals differential enrichment for host transcripts depending on the anatomical site (A) A schematic of the workflow. Ocular tissues were harvested 24 h post challenge with 1 × 10 6 CFUs of PAO1. Tissues were paraffin embedded, sectioned, stained for morphological markers, and hybridized with the whole host transcriptome probe library. ROIs were selected to encompass the epithelial layer, stromal layer, and AC of the eye. Probes were cleaved post hybridization, collected with GeoMx, and amplified, and the generated libraries were sequenced. The image was generated with BioRender. (B) Representative immunohistochemical images of noninfected (contralateral control eyes) and P. aeruginosa -infected ocular tissues stained for cytokeratin (green), Ly6G (red), DNA (blue), and c-KIT (yellow) were visualized with GeoMx (scale bars, 300 μm; n = 2 biological replicas). Robust neutrophil infiltration (red) in the corneal stroma and epithelium is readily observed in the infected site. (C) Volcano plots illustrating differentially expressed transcripts in epithelium and stroma tissue layers of the eye following infection compared to tissues of the non-infected contralateral eye 24 h post challenge. Data are presented cumulatively and derived from biological replicates. The analyzed tissue segments include 16 epithelial ROIs and 16 stromal ROIs collected from 2 biological replicas with 2 technical replicas each. The control contralateral ocular tissue analysis included 8 epithelial ROIs and 8 stromal ROIs from 2 technical replicas. The x axis indicates fold change (log2 scale), and the y axis shows the statistical significance (−log10 false discovery rate [FDR]-adjusted p values). Sample metadata are included. (D) Bar plot of GO (Gene Ontology) functional enrichment analysis, highlighting tissue site-specific gene transcript clustering at level 7. The x axis displays the FDR-adjusted p values (−log10 scale), indicating the statistical significance of the enrichment. The y axis lists the level 7 GO categories with enriched transcripts. This analysis incorporates data from ROI profiles comprising 16 epithelial and 16 stromal samples from ocular tissues harvested 24 h post challenge ( n = 2 biological replicas, n = 2 technical replicas per biological sample) and 8 epithelial and 8 stromal samples from control samples ( n = 2, technical replicas). Data are presented cumulatively and are derived from biological replicates. GO enrichment analysis is listed in Table S1 .

Article Snippet: Ly6G , Novus Biologicals , Clone: 1A8 NB253131AFD PRID:AB2572720.

Techniques: Infection, Staining, Hybridization, Amplification, Generated, Immunohistochemical staining, Control, Derivative Assay, Functional Assay

Journal: Cell Genomics

Article Title: Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors

doi: 10.1016/j.xgen.2025.100805

Figure Lengend Snippet: Bacterial transcript profiling of P. aeruginosa -infected corneas reveal differential tissue enrichment (A) Heatmap showing the distribution of 100 bacterial transcripts in corneas infected with the P. aeruginosa ExoS-expressing strain PAO1. Each column represents data from individual ROIs. Data are presented cumulatively and derived from measurements of 2 biological and 2 technical replicas. Surface epithelial ROIs ( n = 14 ROIs, N = 2 biological replicas, n = 2 technical replicas per biological sample) (green), stromal ROIs ( n = 16 ROIs, n = 2 biological replicas, n = 2 technical replica per biological sample) (yellow), and anterior chamber (AC) ROIs ( n = 16, n = 2 biological replicas, n = 2 technical replicas per biological sample) (purple) are grouped together. The curved lines at the top of the heatmap connect juxtaposing ROIs. (B) Immunohistochemistry analysis of infected corneal sections stained for cytokeratin (green) and Ly6G+ neutrophils (red). Scale bar, 0.5 mm. Also shown is an overlay plot of host and bacterial transcript levels in PAO1-infected tissues. Logarithmic transcript abundances (log2(count + 1)) of host TNF-α and bacterial PA2590, F fpvB , rplL , and a AlgE are represented as circles, where the diameter reflects transcript numbers in the individual ROIs. (C) Bacterial enrichment was calculated as relative transcript abundance in the surface segments compared to the stromal segments. Bacterial transcript levels were normalized to housekeeping bacterial rRplL transcripts. FDR values and fold change (FC) are annotated per gene. Representative bacterial enrichment data depict (1) transcripts that were enriched in the stroma fpvB , PA2590, and femA ; (2) transcripts showing no enrichment; and (3) transcripts showing decreased abundance, such as algE and piv . Complete enrichment analysis is provided in Table S4 .

Article Snippet: Ly6G , Novus Biologicals , Clone: 1A8 NB253131AFD PRID:AB2572720.

Techniques: Infection, Expressing, Derivative Assay, Immunohistochemistry, Staining

Journal: Cell Genomics

Article Title: Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors

doi: 10.1016/j.xgen.2025.100805

Figure Lengend Snippet: Bacterial transcript profiling of PA14-infected corneas (A) Heatmap showing the distribution of 100 bacterial transcripts in uninfected and PA14-infected eyes. The sham (uninfected) and infected tissues were harvested and processed 48 h post challenge. Each column represents data from an individual ROI. Transcript abundance was compared between surface epithelial sham ROIs ( n = 6 ROIs and n = 2 technical replicas) (green), stromal uninfected ROIs ( N = 4 and N = 2 technical replicas) (yellow), and infected surface (epithelial) ROIs ( N = 11 ROIs consisting of 2 or 3 surface ROIs per ocular section, n = 3 biological replicas and up to 2 technical replicas per biological sample) (green), infected stromal ROIs ( n = 11 ROIs comprising 2 or 3 surface ROIs per ocular section, n = 3 biological replicas and up to 2 technical replicas per biological sample) (yellow), and infected AC ROIs ( n = 8 consisting of 2 AC ROIs per ocular section and n = 2 biological replicas with 2 technical replicas per biological sample) (purple) are grouped together. (B) Bacterial enrichment was calculated as relative transcript abundance in the surface (epithelial) segments compared to the stromal segments. Bacterial transcript levels were normalized to the housekeeping bacterial rplL transcripts. FDR values and FC are annotated for fpvB , PA2590, and femA . Complete enrichment analysis is provided in Table S5 . (C) Immunohistochemistry analysis of uninfected and PA14-infected corneal sections stained for OprI (yellow), cytokeratin (green), Ly6G+ neutrophils (red), and DNA (blue). Scale bar, 0.1 mm. Arrows indicate bacterial invasion from the surface lesion into the corneal stroma. Data are representative from sham ( n = 3) and infected tissue ( n = 11) biological replicates. (D) Venn diagram depicting differentially present and shared bacterial transcripts that are enriched within the PAO1- and PA14-infected tissues. FDR values ≤ 0.1.

Article Snippet: Ly6G , Novus Biologicals , Clone: 1A8 NB253131AFD PRID:AB2572720.

Techniques: Infection, Immunohistochemistry, Staining

Journal: Cell Genomics

Article Title: Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors

doi: 10.1016/j.xgen.2025.100805

Figure Lengend Snippet:

Article Snippet: Ly6G , Novus Biologicals , Clone: 1A8 NB253131AFD PRID:AB2572720.

Techniques: Virus, Recombinant, Software