{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Meng Wang"],"organism":["Pseudomonas aeruginosa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16928"],"description":["Pseudomonas aeruginosa is an opportunistic pathogen that can cause severe infections in immunocompromised individuals, such as patients with cystic fibrosis where it commonly forms biofilms. Ciprofloxacin is used extensively to treat P. aeruginosa infections, but its effectiveness can be significantly reduced due to biofilm formation. Although many individual genes associated with biofilm formation have been characterised, the genetic basis of P. aeruginosa biofilm fitness related to antibiotics challenge remain unexplored. In this study we employed a high-density TraDIS-Xpress library of P. aeruginosa PAO1 to assay the impact of gene disruptions or altered gene expression on biofilm formation at different concentrations of ciprofloxacin. Gene fitness was analysed by comparing the biofilm samples to planktonic samples harvested at 12h, 24h and 48h with and without ciprofloxacin. Gene determinants of survival for biofilms at different stages of maturity in the presence and absence of ciprofloxacin were identified."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The biofilm and planktonic samples in this study were recovered from the same bacterial culture grown in 6-well plates. Briefly, the P. aeruginosa transposon mutant library was inoculated (5 μl) into 9 mL of Mueller Hinton (MH) broth to achieve a final concentration of ~5x10^5CFU/mL. Sterile glass beads (~5mm diameter; Sigma-Aldrich) were added to each well (35 sterile per well) serving as substrates for biofilm formation. Plates were incubated at 37 °C at 60 rpm in a humidified chamber. After 12h, 24h and 48h of incubation, biofilm samples and planktonic samples of three independent replicates were collected for DNA extraction. For each replicate, identical cultures in two wells were combined. Planktonic cells from 3 mL of culture were harvested by sedimentation, and pellets were washed by sterile PBS for DNA extraction. For biofilm cells, glass beads collected from two wells were dip-washed with PBS to remove loosely attached cells. Biofilm-associated cells attached to the beads were then resuspended in PBS by vertexing and pelleted by centrifugation at 10000x g for 1 min. Ciprofloxacin was added to the culture medium at the required concentration at the time of inoculation.","Sequencing - DNA fragments were sequenced on a NextSeq500 using the NextSeq 500/550 High Output Kit v2.5 with 75 cycles.","Library Construction - A total of 100 ng of DNA from each sample was fragmented and tagged using the MuSeek Library Preparation Kit (Thermo Scientific). Following a purification step with AMPure XP beads, the DNA fragments containing transposon insertion junctions were selectively enriched by an initial PCR using a pair of custom primers. The first primer was biotinylated and annealed to the transposon sequence and a customed i7 primer annealed to the tagged sequence generated by the Mu transposase. The resulting PCR products were sequentially purified using AMPure XP beads and then streptavidin beads, ensuring high specificity and purification of the target amplicon. A second round of PCR was subsequently performed using custom i5 and i7 primers to incorporate adapter sequences for high-throughput sequencing using the Illumina method.","Nucleic Acid Extraction - Genomic DNA (gDNA) of biofilm and planktonic samples was extracted using the Quick-DNA Fungal/Bacterial Microprep Kit and Miniprep Kit (Zymo research) respectively according to the manufacturer’s instruction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["DNA-seq"],"species":["Pseudomonas aeruginosa"],"pubmed_title":["Identification of genes important for response of Pseudomonas aeruginosa biofilms to ciprofloxacin exposure"],"pubmed_authors":["Meng Wang"],"additional_accession":[]},"is_claimable":false,"name":"Identification of genes important for response of Pseudomonas aeruginosa biofilms to ciprofloxacin exposure using TraDIS-Xpress","description":"Pseudomonas aeruginosa is an opportunistic pathogen that can cause severe infections in immunocompromised individuals, such as patients with cystic fibrosis where it commonly forms biofilms. Ciprofloxacin is used extensively to treat P. aeruginosa infections, but its effectiveness can be significantly reduced due to biofilm formation. Although many individual genes associated with biofilm formation have been characterised, the genetic basis of P. aeruginosa biofilm fitness related to antibiotics challenge remain unexplored. In this study we employed a high-density TraDIS-Xpress library of P. aeruginosa PAO1 to assay the impact of gene disruptions or altered gene expression on biofilm formation at different concentrations of ciprofloxacin. Gene fitness was analysed by comparing the biofilm samples to planktonic samples harvested at 12h, 24h and 48h with and without ciprofloxacin. Gene determinants of survival for biofilms at different stages of maturity in the presence and absence of ciprofloxacin were identified.","dates":{"release":"2026-06-09T00:00:00Z","modification":"2026-06-11T11:19:05.883Z","creation":"2026-04-17T11:44:53.402Z"},"accession":"E-MTAB-16928","cross_references":{"ENA":["ERP192295"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0004184"]}}