READ ME File For 'Strain-specific Intracellular Staphylococcus aureus in resistant chronic rhinosinusitis. Disease mechanisms and potential novel therapies' Dataset DOI: 10.5258/SOTON/D2509 Date that the file was created: 04, 2024 ------------------- GENERAL INFORMATION ------------------- ReadMe Author: Simon Goldie, University of Southampton [0000-0002-3912-9026] Date of data collection: 01/03/2018-01/06/2023 Information about geographic location of data collection: Collected at University Hospital Southampton Related projects: British Rhinological Society research grant 2019 RCSEng research fellowship 2020 RCSEd pump priming grant SPPG/21/158 -------------------------- SHARING/ACCESS INFORMATION -------------------------- Licenses/restrictions placed on the data, or limitations of reuse: CC BY license This dataset supports the publication: AUTHORS: Goldie SP TITLE: Strain-specific Intracellular Staphylococcus aureus in resistant chronic rhinosinusitis. Disease mechanisms and potential novel therapies JOURNAL: PhD Thesis -------------------- DATA & FILE OVERVIEW -------------------- This dataset contains: 4 files with S.aureus sequences cultured from control subjects (control_strains.zip), CRSsNP subjects (CRSsNP_strains.zip) and CRSwNP subjects (CRSwNP_strains.zip) and all remaining PhD date (PhD_Data_zip.zip Control_Strains file: Control1_R1.fastq.gz Read 1 of control 1 S.aureus in FASTQ format Control1_R2.fastq.gz Read 2 of control 1 S.aureus in FASTQ format Control2_R1.fastq.gz Read 1 of control 2 S.aureus in FASTQ format Control2_R2.fastq.gz Read 2 of control 2 S.aureus in FASTQ format Control3_R1.fastq.gz Read 1 of control 3 S.aureus in FASTQ format Control3_R2.fastq.gz Read 2 of control 3 S.aureus in FASTQ format Control4_R1.fastq.gz Read 1 of control 4 S.aureus in FASTQ format Control4_R2.fastq.gz Read 2 of control 4 S.aureus in FASTQ format Control5_R1.fastq.gz Read 1 of control 5 S.aureus in FASTQ format Control5_R2.fastq.gz Read 2 of control 5 S.aureus in FASTQ format CRSsNP_strains file: CRSsNP1_R1.fastq.gz Read 1 of CRSsNP 1 S.aureus in FASTQ format CRSsNP1_R2.fastq.gz Read 2 of CRSsNP 1 S.aureus in FASTQ format CRSsNP2_R1.fastq.gz Read 1 of CRSsNP 2 S.aureus in FASTQ format CRSsNP2_R2.fastq.gz Read 2 of CRSsNP 2 S.aureus in FASTQ format CRSsNP3_R1.fastq.gz Read 1 of CRSsNP 3 S.aureus in FASTQ format CRSsNP3_R2.fastq.gz Read 2 of CRSsNP 3 S.aureus in FASTQ format CRSsNP4_R1.fastq.gz Read 1 of CRSsNP 4 S.aureus in FASTQ format CRSsNP4_R2.fastq.gz Read 2 of CRSsNP 4 S.aureus in FASTQ format CRSwNP_Strains File: CRSwNP1_R1.fastq.gz Read 1 of CRSwNP 1 S.aureus in FASTQ format CRSwNP1_R2.fastq.gz Read 2 of CRSwNP 1 S.aureus in FASTQ format CRSwNP2_R1.fastq.gz Read 1 of CRSwNP 2 S.aureus in FASTQ format CRSwNP2_R2.fastq.gz Read 2 of CRSwNP 2 S.aureus in FASTQ format CRSwNP3_R1.fastq.gz Read 1 of CRSwNP 3 S.aureus in FASTQ format CRSwNP3_R2.fastq.gz Read 2 of CRSwNP 3 S.aureus in FASTQ format CRSwNP4_R1.fastq.gz Read 1 of CRSwNP 4 S.aureus in FASTQ format CRSwNP4_R2.fastq.gz Read 2 of CRSwNP 4 S.aureus in FASTQ format PhD_Data_Zip file contains Chapter_2-growth_curves_for_s.aureus.xlsx Microsoft Excel file demonstrating growth curves for Control 1 and CRSwNP 1 S.aureus strains used in further experiments Chapter_3-Anonymous_sample_log_.xlsx Microsoft excel file of sample log depicting demographics of subjects involved in the study Chapter_3-agrvateoutput.tsv Text file demonstrating Bactopia output of AGR type analysis Chapter_3-Spatyperoutput.tsv Text file of bactopia output of Staphylococcal protein A program (SPAtyper) Chapter_3-armfinderplus_proteinoutput.csv Comma separated value file demonstrating Bactopia ARMfinderplus output (shows virulence and antimicrobial resistance gene output) Chapter_3-armfinderplus_proteinoutput.csv Comma separated value file demonstrating Bactopia ARMfinderplus output (shows virulence and antimicrobial resistance gene output) Chapter_4-HMC1_survivaldata.pzfx Graphpad Prism file demonstrating extra and intracellular survival of a control and CRSwNP S.aureus in HMC1 cell culture Chapter_4-LAD2_survivaldata.pzfx Graphpad Prism file demonstrating extra and intracellular survival of a control and CRSwNP S.aureus in LAD2 cell culture Chapter_4-Betahex_LDH_assay.pzfx Graphpad Prism file demonstrating LDH and beta-hexosaminidase release from LAD2 cells in co-culture with control and CRSwNP S.aureus Chapter_4-Live_dead_confocal_images.tif Tag image file demonstrating Live/dead images of LAD2 cells treated with control and CRSwNP S.aureus Chapter_5-SimvastatinMICcalculation.pzfx Graphpad Prism file depicting minimal inhibitory concentration calculation for prodrug and activated simvastatin Chapter_5-Intracellular_S.aureus_in_lad2_treated_with_serumsimvastatin.pzfx Graphpad Prism file of Intracellular survival of S.aureus in LAD2 cells treated with simvastatin at serum concentrations Chapter_5-IntracellularSaureus_survivalvssimvastatin.pzfx Graphpad Prism file of intracellular survival of S.aureus when treated with increased doses of simvastatin Chapter_5-LAD2_Saureus_simvastatin_confocal.pdf Adobe PDF image depicting confocal microscopy findings of LAD2 cells treated with simvastatin Chapter_5-Confocal_intracellular_S.aureus_calculation.pzfx Graphpad Prism file of numerical calculation of S.aureus infection rates of LAD2 cells in the presence of Simvastatin Chapter_5-degranulationassaycubpc48_80.pzfx Graphpad Prism file of degranulation of lad 2 cells when exposed to substance P and Compound 48/40 Chapter_5-ALI_TEER_saureus_statin.pzfx Graphpad Prism file of Trans epithelial resistance change of ALI treated with S.aureus, Simvastatin and both Chapter_5-ALIFISH.pdf Adobe PDF showing fluorescence in situ hybridisation of ALI cultures treated with S. aureus and simvastatin Chapter-5-ALIstatinQPCToutput.xlsx Microsoft excel file of quantative Raw PCR data assessing epithelial cytokine release of AlI treated with S.aureus and Simvastatin Chapter_5-ALIcytokine_expression.pzfx Graphpad Prism file of PCR data assessing epithelial cytokine release of AlI treated with S.aureus and Simvastatin -------------------------- METHODOLOGICAL INFORMATION -------------------------- All Methods used to collect and process this data are present in Strain-specific Intracellular Staphylococcus aureus in resistant chronic rhinosinusitis. Disease mechanisms and potential novel therapies data, PhD Thesis, University of Southampton, Simon Goldie -------------------------- DATA-SPECIFIC INFORMATION -------------------------- Within PhD Data_zip: Chapter_3-agrvateoutput.tsv Commensal represents control 1 strain, P3 strain represents CRSwNP1 strain Chapter_3-Spatyperoutput.tsv Commensal represents control 1 strain, P3 strain represents CRSwNP1 strain Chapter-5-ALIstatinQPCToutput.xlsx HKG = house keeping gene, GOI = gene of interest, dCt = delta cycle threshold ddCt = delta delta cycle threshold --------------