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Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces

ABSTRACT: Purpose: Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces. Methods: Coupons of silicone, glass, and polycarbonate plastic were purchased from Biosurfaces Technologies (Catalog numbers: RD128-Si, RD128-GL, RD128-PC). Coupons were placed into a 24-well plate and conditioned in LB for at least 10 min prior to bacterial addition. LB was removed and replaced with 2mL of logarithmic phase bacterial culture in LB (OD600 0.7). At the indicated time point, the coupon was rinsed twice in PBS and placed into 1 mL of Trizol. Trizol was collected and stored at -80°C for RNA isolation. HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads. Reads were aligned to the reference PAO1 genome using Rockhopper. Results: A total of 833 genes were differentially expressed across the three surfaces. Most genes were reduced (522 genes) rather than elevated (269 genes), with 42 genes showing both elevated and reduced RNA levels across two or more surfaces. Conclusion: Bacteria had a nearly unique transcriptional response on each surface, with the vast majority regulated on only one surface

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE195826 | GEO | 2022/02/03

REPOSITORIES: GEO

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Project description:The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column. Experimenter name = Martin Broadley Experimenter phone = 0115 951 6382 Experimenter fax = 0115 951 6334 Experimenter institute = University of Nottingham Experimenter address = Plant Sciences Division Experimenter address = School of Biosciences Experimenter address = University of Nottingham Experimenter address = Sutton Bonington Experimenter address = Loughborough Experimenter zip/postal_code = LE12 5RD Experimenter country = UK Keywords: growth_condition_design

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Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces

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