biostudies-arrayexpressClaire BroderickHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15137We aimed to test the hypothesis that influenza infection of healthy adults alters whole blood mycobacterial control through modulation of anti-mycobacterial immune responses. We employed a whole blood mycobacterial growth inhibition assay within the framework of a human influenza challenge study. We utilised a recombinant reporter strain of mycobacteria, Mycobacterium bovis Bacille Calmette Guerin (BCG) lux, whose luminescence provides a quantitative read-out of live mycobacteria present. Volunteers were challenged with Influenza A (H3N2) virus and infection confirmed by qPCR of nasal lavage samples. Blood aliquots, taken from participants before and after influenza infection, were infected with BCG lux and incubated for up to 72 hours (0, 6, 24, 72 h). BCG-uninfected blood aliquots were also incubated. Whole blood mycobacterial growth and transcriptomic, cytokine and cellular responses to mycobacterial infection were measured in parallel and compared in the same subjects, before versus after influenza infection.biostudies-arrayexpressSequencing - Paired end sequencing was performed at the Oxford Genomics Centre using a Novaseq6000 platform (Illumina, CA, USA) at 150 paired end configuration.Nucleic Acid Extraction - RNA was extracted using the PAXgene® blood miRNA kit (PreAnalytix) according to the manufacturer’s manual extraction protocol, with on-column DNase treatment and clean-up using RNA Clean & Concentrator-5 kit (Zymo Research, CA, USA).Library Construction - Strand specific library preparation was completed using NEBNext® Ultra™ II mRNA kit (New England BioLabs [NEB], MA, USA) and NEB human v2 rRNA/globin depletion probes (NEB) following the manufacturer’s instructions.Sample Collection - Whole blood was collected in a Lithiuim heparin tube and diluted 50:50 with RPMI 1640/ 2 mM glutamine medium (GibcoTM, Thermo Fisher). Aliquots were infected with BCG lux (colony forming unit: monocyte MOI of 1:1) and incubated in a rocking incubator for up to 72 h. For BCG-uninfected aliquots, PBS was added. At the appropriate timepoint, the sample was removed from the incubator, centrifuged at 2000 g for 10 minutes and the supernatant carefully removed. To the cell pellet, RNA preservative from a PAXgene® tube (PreAnalytix, GmBH, Switzerland) was added at a ratio of 2.76: 1 undiluted whole blood, as recommended by the manufacturer. The sample was vortexed to disperse the cell pellet and then frozen at -20 °C overnight before being transferred to -80 °C for longer term storageOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Quality control was performed using FastQC and MultiQC and annotations were modified with BEDTools. Alignment against hg38 reference genome version was undertaken using STAR and SAMtools, followed by transcript quantification using featureCounts.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsRIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensClaire BroderickMyrsini KaforoufalseWhole blood RNA-sequencing from volunteers in a human influenza challenge study, in which blood aliquots were infected and incubated with BCG before and after influenza infectionWe aimed to test the hypothesis that influenza infection of healthy adults alters whole blood mycobacterial control through modulation of anti-mycobacterial immune responses. We employed a whole blood mycobacterial growth inhibition assay within the framework of a human influenza challenge study. We utilised a recombinant reporter strain of mycobacteria, Mycobacterium bovis Bacille Calmette Guerin (BCG) lux, whose luminescence provides a quantitative read-out of live mycobacteria present. Volunteers were challenged with Influenza A (H3N2) virus and infection confirmed by qPCR of nasal lavage samples. Blood aliquots, taken from participants before and after influenza infection, were infected with BCG lux and incubated for up to 72 hours (0, 6, 24, 72 h). BCG-uninfected blood aliquots were also incubated. Whole blood mycobacterial growth and transcriptomic, cytokine and cellular responses to mycobacterial infection were measured in parallel and compared in the same subjects, before versus after influenza infection.2026-06-11T00:00:00Z2026-06-11T01:00:50.319Z2025-05-18T14:17:56.319ZE-MTAB-15137EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184