This readme.txt file was generated on 20240802 by Guanju Wei Recommended citation for the data: Wei, Guanju; Yang, Judy Q. (2024). Data supporting Motility directs Pseudomonas aeruginosa towards surfaces and enhances biofilm formation. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/tq68-ww73. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data supporting Motility directs Pseudomonas aeruginosa towards surfaces and enhances biofilm formation 2. Author Information Principal Investigator Contact Information Name: Guanju Wei Institution: Saint Anthony Falls Laboratory, University of Minnesota Address: 2 3rd Ave SE, Minneapolis, MN 55414 Email: wei00235@umn.edu ORCID: 0000-0001-5511-9242 Associate or Co-investigator Contact Information Name: Judy Q. Yang Institution: Saint Anthony Falls Laboratory, University of Minnesota Address: 2 3rd Ave SE, Minneapolis, MN 55414 Email: judyyang@umn.edu ORCID: 0000-0001-6272-1266 3. Date published or finalized for release: 20240802 4. Date of data collection (single date, range, approximate date) 20240128-20240526 5. Geographic location of data collection (where was data collected?): Saint Anthony Falls Laboratory, University of Minnesota 6. Information about funding sources that supported the collection of the data: This study was supported by National Science Foundation CAREER Award EAR 2236497. Portions of this work were conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nanotechnology Coordinated Infrastructure (NNCI) under Award Number ECCS-2025124. We thank Dr. J. Sanfilippo for his generosity in helping with the bacterial strains. 7. Overview of the data (abstract): This dataset supports the manuscript “Motility directs Pseudomonas aeruginosa towards surfaces and enhances biofilm formation”. It contains all the angles and trajectories for both motile and non-motile Pseudomonas aeruginosa cells. In the manuscript, we demonstrated that the cell motility can enhance biofilm formation and utilized the orientation angle and trajectory data to support this conclusion. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Manuscript under review. 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use Yes. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Motile (folder) Short description: This folder contains trajectory information for motile P. aeruginosa cells at various flow rates. Each .xlsx file is labeled according to the specific flow rate it represents. B. Filename: Non-motile (folder) Short description: This folder contains trajectory information for non-motile P. aeruginosa cells at various flow rates. Each .xlsx file is labeled according to the specific flow rate it represents. C. Filename: Image_Processing_Code. txt Short description: Matlab codes used to generate the trajectory and calculate the probability distribution of angles. 2. Relationship between files: These two folders contain data for the trajectory information for motile and non-motile P. aeruginosa cells during the same biofilm development experiments. The .xlsx flies in each folder represent one flow rate. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: The experimental system consists of a microfluidic chip, a Confocal Laser Scanning Microscope (C2 plus, Nikon, Japan), a high-speed camera (ORCA-FLASH 4.0, Hamamatsu Photonics, Japan), and a programmable syringe pump (PHD Ultra, Harvard Apparatus). Soft lithography was used to fabricate polydimethylsiloxane (PDMS) microfluidic chips with the assistance of the University of Minnesota Nano Center. The straight channels utilized in this study have a height of 60 μm and a width of 400 μm. The channel measures 5 mm in length from inlet to outlet. The PDMS channel is bonded to a #1.5 cover glass (Electron Microscopy Sciences, USA) using a corona plasma treater (Electro-Technic Products, USA) for a 30-second surface treatment. All the experiments were conducted under room temperature (~22 °C) to minimize cell growth as this study primarily focuses on investigating the swimming and attachment behaviors of cells. Biofilm development experiments were conducted following the steps described below. First, 2 mL of nutrient solution (abiotic M9 solution containing 1 wt.% D-glucose) was injected into the microfluidics to displace the air in the channel. Then, we continuously injected Pseudomonas aeruginosa bacterial solution (OD600 = 0.51 ± 0.02) into the microfluidic channel at five different flow rates (Q = 0.5, 1, 2.5, 5, and 10 μl/min) for 15 hours. 2. Methods for processing the data: The trajectories and cell wall-normal angle were calculated using the TrackMate function in ImageJ. Specifically, we employed the Thresholding detector and Nearest-neighbor tracker to detect the cell movements. Cell trajectories were reconstructed in MATLAB. The cell wall-normal angle was derived from the ellipse angle in ImageJ following a coordinate transformation. Additionally, these angles were subjected to manual verification to ensure accuracy. 3. Instrument- or software-specific information needed to interpret the data: Matlab, ImageJ, Excel 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: P. aeruginosa cells were cultured from a frozen stock and incubated them in Luria Broth (LB) solution overnight (~16 h), at 37 °C with 200 rpm shaking. 6. Describe any quality-assurance procedures performed on the data: For each experimental condition, three biological replicates were conducted. 7. People involved with sample collection, processing, analysis and/or submission: Guanju Wei (sample collection, processing, analysis, submission) Judy Yang (analysis, submission) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [JS11_0.5ulmin.xlsx.] ----------------------------------------- All the .xlsx files follow the same format. Here is an example: JS11_0.5ulmin.xlsx. 1. Number of variables: 7 2. Number of cases/rows: 4860, each rows represent a cell spot. 3. Missing data codes: N/A 4. Variable List A. Name: Description: each spot ID derived from ImageJ. C. Name: Description: The trajectory ID. E. Name: , , Description: The x, y, z coordinates for each spot. Used for generate trajectory. F. Name: Description: The time frame for each spot. G. Name: < El. angle> Description: Cell orientation angle. ------------------------------- DATA TREE ------------------------------- \---Angle and Trajectory Data.zip | Image_Processing_Code.txt | +---Motile | JS11_0.5ulmin.xlsx | JS11_0.5ulmin_2.xlsx | JS11_10ulmin.xlsx | JS11_10ulmin_2.xlsx | JS11_1ulmin.xlsx | JS11_1ulmin_2.xlsx | JS11_1ulmin_3.xlsx | JS11_2.5ulmin.xlsx | JS11_2.5ulmin_2.xlsx | JS11_5ulmin.xlsx | JS11_5ulmin_2.xlsx | JS11_5ulmin_3.xlsx | JS11_noflow.xlsx | \---Non_motile JS204_10ulmin.xlsx JS204_10ulmin_2.xlsx JS204_1ulmin.xlsx JS204_1ulmin_2.xlsx JS204_1ulmin_3.xlsx JS204_2.5ulmin.xlsx JS204_2.5ulmin_2.xlsx JS204_5ulmin.xlsx JS204_5ulmin_2.xlsx