Fig. 1: RNA-seq analysis reveals common and pathogen-specific immune-regulatory lncRNA expression profiles in THP-1 macrophages across bacterial infections.

a Principal component analysis (PCA) of RNA-seq data illustrating transcriptional variance across infections, including C. burnetii Nine Mile Phase II (Cb), C. burnetii Nine Mile Phase II dotA::Tn (CbA), C. burnetii Nine Mile Phase II dotB::Tn (CbB), Escherichia coli DH5α (Ec5), enterohemorrhagic E. coli O157 (EcT/EHEC), E. coli O157Δstx (EcN/EHECΔstx), Bacillus subtilis P31K6 (Bs), Francisella novicida U112 (Fn), Pseudomonas aeruginosa PAO1 (Pa), Staphylococcus aureus JE2 (Sa), Salmonella enterica subsp. Typhimurium SL1344 (STm), Rhizobium radiobacter (Rr), Micrococcus luteus (Ml), Listeria innocua (Li), Enterococcus faecalis (Ef), and Brucella melitensis ΔvjbR (Bmv). PCA was performed using normalized RNA-seq data to assess global transcriptional variance. Infected samples are denoted by circles; mock-infected controls as triangles. Data points are color-coded by infection. b Experimental workflow for identifying common and pathogen-specific lncRNAs following infection of THP-1 macrophages. Schematics created using BioRender.com. c Bar graph summarizing the number of pathogen-specific differentially expressed (DE) lncRNAs identified across the infections analyzed. d Heatmap showing quantitative real-time PCR (RT-qPCR) validation of selected immune-regulatory lncRNAs that are either commonly regulated across infections or specifically altered during C. burnetii infection. Expression normalized to ACTB and shown relative to mock-infected controls (set to 1). lncRNAs with a log₂ fold change ≥ 1.5 or ≤ 0.5 were considered DE. Data represent mean ± SD from three independent experiments (n = 3). Source data are provided as a Source Data file.