Source data and representative raw data for "Peptidoglycan synthesis drives a single population of septal cell wall synthases during division in Bacillus subtilis"

<h2>READ ME</h2> <h2>General information</h2> <p>Author: Kevin Whitley</p> <p>Contact: kevin.whitley@newcastle.ac.uk</p> <p>DOI: https://doi.org/10.25405/data.ncl.c.7078312</p> <p>Related article: K.D. Whitley, J. Grimshaw, D.M. Roberts, E. Karinou, P.J. Stansfeld, S. Holden. Peptidoglycan synthesis drives a single population of septal cell wall synthases during division in Bacillus subtilis. Nature Microbiology (2024). <a href="https://doi.org/10.1038/s41564-024-01650-9" target="_blank">https://doi.org/10.1038/s41564-024-01650-9</a> </p> <p><br></p> <h2>Introductory information</h2> <p>The following contain source data. This includes some of the figures in MATLAB .fig format, underlying data in .xlsx format, along with the videos and accompanying kymographs that are shown in the figures:</p> <p>1) <a href="https://doi.org/10.25405/data.ncl.25225364" target="_blank">Figure 1 source data</a></p> <p>2) <a href="https://doi.org/10.25405/data.ncl.25225676" target="_blank">Figure 2 source data</a></p> <p>3) <a href="https://doi.org/10.25405/data.ncl.25225952" target="_blank">Figure 3 source data</a></p> <p>4) <a href="https://doi.org/10.25405/data.ncl.25226003" target="_blank">Figure 4 source data</a></p> <p>5) <a href="https://doi.org/10.25405/data.ncl.25226105" target="_blank">Supplementary Figure 1 source data</a></p> <p>6) <a href="https://doi.org/10.25405/data.ncl.25226174" target="_blank">Supplementary Figure 2 source data</a></p> <p>7) <a href="https://doi.org/10.25405/data.ncl.25226189" target="_blank">Supplementary Figure 3 source data</a></p> <p>8) <a href="https://doi.org/10.25405/data.ncl.25226273" target="_blank">Supplementary Figure 4 source data</a></p> <p>9) <a href="https://doi.org/10.25405/data.ncl.25226333" target="_blank">Supplementary Figure 5 source data</a></p> <p>10) <a href="https://doi.org/10.25405/data.ncl.25226453" target="_blank">Supplementary Figure 6 source data</a></p> <p>11) <a href="https://doi.org/10.25405/data.ncl.25226558" target="_blank">Supplementary Figure 7 source data</a></p> <p>12) <a href="https://doi.org/10.25405/data.ncl.25226588" target="_blank">Supplementary Figure 8 source data</a></p> <p>13) <a href="https://doi.org/10.25405/data.ncl.25226603" target="_blank">Supplementary Figure 9 source data</a></p> <p>14) <a href="https://doi.org/10.25405/data.ncl.25226666" target="_blank">Supplementary Figure 10 source data</a></p> <p>15) <a href="https://doi.org/10.25405/data.ncl.25226690" target="_blank">Supplementary Figure 11 source data</a></p> <p>16) <a href="https://doi.org/10.25405/data.ncl.25226303" target="_blank">Extended Data Figure 2 source data</a></p> <p>17) <a href="https://doi.org/10.25405/data.ncl.25226345" target="_blank">Extended Data Figure 3 source data</a></p> <p>18) <a href="https://doi.org/10.25405/data.ncl.25226462" target="_blank">Extended Data Figure 4 source data</a></p> <p>19) <a href="https://doi.org/10.25405/data.ncl.25226627" target="_blank">Extended Data Figure 5 source data</a></p> <p>20) <a href="https://doi.org/10.25405/data.ncl.25226711" target="_blank">Extended Data Figure 6 source data</a></p> <p>21) <a href="https://doi.org/10.25405/data.ncl.25226777" target="_blank">Extended Data Figure 7 source data</a></p> <p>22) <a href="https://doi.org/10.25405/data.ncl.25226858" target="_blank">Extended Data Figure 8 source data</a></p> <p>23) <a href="https://doi.org/10.25405/data.ncl.25226891" target="_blank">Extended Data Figure 9 source data</a></p> <p>24) <a href="https://doi.org/10.25405/data.ncl.25226933" target="_blank">Extended Data Figure 10 source data</a></p> <p><br></p> <p>The following contain videos corresonding to the Supplementary Videos in the manuscript. They contain .avi files, as well as the more raw .tif or .nd2 files:</p> <p>25) <a href="https://doi.org/10.25405/data.ncl.25229345" target="_blank">Supplementary Video 1 source data</a></p> <p>26) <a href="https://doi.org/10.25405/data.ncl.25229381" target="_blank">Supplementary Video 2 source data</a></p> <p>27) <a href="https://doi.org/10.25405/data.ncl.25229384" target="_blank">Supplementary Video 3 source data</a></p> <p>28) <a href="https://doi.org/10.25405/data.ncl.25229390" target="_blank">Supplementary Video 4 source data</a></p> <p>29) <a href="https://doi.org/10.25405/data.ncl.25229393" target="_blank">Supplementary Video 5 source data</a></p> <p>30) <a href="https://doi.org/10.25405/data.ncl.25229396" target="_blank">Supplementary Video 6 source data</a></p> <p>31) <a href="https://doi.org/10.25405/data.ncl.25229402" target="_blank">Supplementary Video 7 source data</a></p> <p>32) <a href="https://doi.org/10.25405/data.ncl.25229408" target="_blank">Supplementary Video 8 source data</a></p> <p>33) <a href="https://doi.org/10.25405/data.ncl.25229531" target="_blank">Supplementary Video 9 source data</a></p> <p>34) <a href="https://doi.org/10.25405/data.ncl.25229540" target="_blank">Supplementary Video 10 source data</a></p> <p>35) <a href="https://doi.org/10.25405/data.ncl.25229543" target="_blank">Supplementary Video 11 source data</a></p> <p>36) <a href="https://doi.org/10.25405/data.ncl.25229546" target="_blank">Supplementary Video 12 source data</a></p> <p>37) <a href="https://doi.org/10.25405/data.ncl.25229552" target="_blank">Supplementary Video 13 source data</a></p> <p>38) <a href="https://doi.org/10.25405/data.ncl.25229555" target="_blank">Supplementary Video 14 source data</a></p> <p>39) <a href="https://doi.org/10.25405/data.ncl.25229564" target="_blank">Supplementary Video 15 source data</a></p> <p>40) <a href="https://doi.org/10.25405/data.ncl.25229579" target="_blank">Supplementary Video 16 source data</a></p> <p><br></p> <p>The following contain representative raw data (no processing) for the conditions used in the paper:</p> <p>41) <a href="https://doi.org/10.25405/data.ncl.25232639" target="_blank">Representative raw data for rich media, 30C</a></p> <p>42) <a href="https://doi.org/10.25405/data.ncl.25232657" target="_blank">Representative raw data for rich media, 30C with Penicillin G treatment</a></p> <p>43) <a href="https://doi.org/10.25405/data.ncl.25232684" target="_blank">Representative raw data for rich media, 30C with fosfomycin treatment</a></p> <p>44) <a href="https://doi.org/10.25405/data.ncl.25232699" target="_blank">Representative data for rich media, 37C</a></p> <p>45) <a href="https://doi.org/10.25405/data.ncl.25232702" target="_blank">Representative data for minimal media, 30C</a></p> <p>46) <a href="https://doi.org/10.25405/data.ncl.25232720" target="_blank">Representative raw data for minimal media, 37C</a></p> <p>47) <a href="https://doi.org/10.25405/data.ncl.25232723" target="_blank">Representative raw data for rich media, 30C with PC190723 treatment</a></p> <p>48) <a href="https://doi.org/10.25405/data.ncl.25232729" target="_blank">Representative raw data for rich media, 30C with FtsZ(G106S) expression</a></p> <p>49) <a href="https://doi.org/10.25405/data.ncl.25232756" target="_blank">Representative raw data for FtsZ treadmilling in Dhag GFP-FtsZ HT-PBP2B strain</a></p> <p>50) <a href="https://doi.org/10.25405/data.ncl.25232795" target="_blank">Representative raw data for rich media, 30C with 1 mM IPTG</a></p> <p>51) <a href="https://doi.org/10.25405/data.ncl.25232804" target="_blank">Representative raw data for FtsZ treadmilling in rich media, 21C</a></p> <p>52) <a href="https://doi.org/10.25405/data.ncl.25232816" target="_blank">Representative raw data for FtsZ(G106S) treadmilling in rich media, 30C</a></p> <p>53) <a href="https://doi.org/10.25405/data.ncl.25232822" target="_blank">Representative raw data for HT-PBP2B motion horizontally in untreated cells</a></p> <p>54) <a href="https://doi.org/10.25405/data.ncl.25232827" target="_blank">Representative raw data for HT-PBP2B motion in horizontal cells with PC190723 treatment</a></p> <p>55) <a href="https://doi.org/10.25405/data.ncl.25232833" target="_blank">Representative raw data for HT-PBP2B motion in horizontal cells with FtsZ(G106S) expression</a></p> <p>56) <a href="https://doi.org/10.25405/data.ncl.25232836" target="_blank">Representative raw data for HaloTag-FtsW motion in rich media, 30C</a></p> <h2>Methodological information</h2> <p>Most raw data in this repository is from fluorescence microscopy on bacteria. Many of the files are videos showing single-molecule dynamics of bacterial cell wall synthases inside live bacteria. Other files are data supporting these, such as characterizations of the bacterial strains used(growth, morphology, etc.).</p> <p>Abbreviations: ROI = Region of Interest.</p> <p>Instruments used: Bespoke single-molecule fluorescence microscope, Nikon Eclipse Ti, Nikon Eclipse Ti2, and Zeiss Elyra 7 Lattice SIM2.</p> <p>Data acquisition software: Data collected using either Micro-Manager (v2.0gamma), NS-Elements (v5.42.02), or Zen Black 2.3 (v16.0.14.316).</p> <p>Data analysis software: Videos analysed using Fiji (v1.54) with open-source plugins PureDenoise-GPU (v0.1.0) and PureDenoise-CPU (v0.1.0) (https://github.com/ZikaiSun/PureGpu/tree/main).</p> <p>Extended Data Figures 4 and 6, along with Supplementary Videos 14-16 show data from molecules manually tracked using TrackMate (v7.10.2).</p> <p>Further data analysis done using Matlab with custom code available on the Whitley lab Github page:</p> <p>https://github.com/WhitleyLab/Vercini_spt_analysis</p> <p>The divisome complex was modelled by AlphaFold2, using ColabFold (v1.3.0) and AlphaFold-Multimer (v2).</p> <p>Date(s) of data collection: 15/12/2021 - 10/12/2023</p> <p><br></p>