biostudies-arrayexpressBurkholderia cenocepaciahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13688In this study, we embark on a journey to unravel the profound impact of atsR (Adherence and T6SS Regulator) gene deletion on the transcriptome and the proteome of B. cenocepacia K56-2 upon growth in synthetic CF medium (SCFM), the most in-vivo-like culturing medium. Our insights, derived from RNA-seq analysis and label-free LC-MS-based proteomics, validated by multiple reaction monitoring (MRM) analysis, reveal that AtsR's influence extends beyond adhesion, T6SS and the two above QSs, encompassing valdiazen QS, phenylacetic acid signaling system, diffusible signaling factor production, and other pathogenesis-modulating elements such as alternative sigma factors, small regulatory RNAs, and several chaperones.biostudies-arrayexpressGrowth Protocol - Cells were grown at 37°C while shaking at 200 rpm in synthetic CF medium (SCFM).Sample Collection - Overnight liquid cultures of each isolate, B. cenocepacia wild type and each mutant, that were grown at 37°C while shaking at 200 rpm in SCFM, were transferred to fresh media until the mid-exponential phase was reached. The cultures were subsequently diluted to a standardized culture to OD600nm 0.4 in 250 ml glass flasks. These cultures were further incubated for 18 hours before centrifugation at 4°C and the obtained cell pellets stored at −80 °C for a maximum of 1 week.Nucleic Acid Extraction - RNA extraction was outsourced to GENEWIZ Europe (Leipzig, Germany).Sequencing - RNA sequencing was outsourced to GENEWIZ Europe (Leipzig, Germany). It was on Illumina 2x15040M paired end reads (20M in each direction) per sampleLibrary Construction - Library prep was outsourced to GENEWIZ Europe (Leipzig, Germany).MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Normalization was performed using Log2_FPKM (Fragments per Kilobase per Million) values to determine the relative abundances between strains, as well as a fold change of ≥1.48 and a P-value of ≤0.01 were the criteria set for reporting differentially expressed genes. The DESeq2 package was also used for differential expression analysis.Sequence Alignment - HISAT2 algorithm was used for the read mapping to the B. cenocepacia J2315 reference genome and StringTie was employed to calculate read counts per feature (transcript). Parallel, READemption pipelines were also used for the thereafter validation of up- and down-regulated gene expression.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq XRNA-seq of coding RNABurkholderia cenocepaciaERP156491Amir HassanfalseRNA-seq data to map the AtsR regulon in B. cenocepaciaIn this study, we embark on a journey to unravel the profound impact of atsR (Adherence and T6SS Regulator) gene deletion on the transcriptome and the proteome of B. cenocepacia K56-2 upon growth in synthetic CF medium (SCFM), the most in-vivo-like culturing medium. Our insights, derived from RNA-seq analysis and label-free LC-MS-based proteomics, validated by multiple reaction monitoring (MRM) analysis, reveal that AtsR's influence extends beyond adhesion, T6SS and the two above QSs, encompassing valdiazen QS, phenylacetic acid signaling system, diffusible signaling factor production, and other pathogenesis-modulating elements such as alternative sigma factors, small regulatory RNAs, and several chaperones.2026-03-31T00:00:00Z2026-03-31T01:03:46.754Z2024-01-05T17:30:44.769ZE-MTAB-13688ERP156491EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184