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

Version 2 2024-03-14, 16:16
Version 1 2024-02-28, 16:41
Posted on 2024-03-14 - 16:16 authored by Kevin Whitley

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General information

Author: Kevin Whitley

Contact: kevin.whitley@newcastle.ac.uk

DOI: https://doi.org/10.25405/data.ncl.c.7078312

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). https://doi.org/10.1038/s41564-024-01650-9 


Introductory information

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:

1) Figure 1 source data

2) Figure 2 source data

3) Figure 3 source data

4) Figure 4 source data

5) Supplementary Figure 1 source data

6) Supplementary Figure 2 source data

7) Supplementary Figure 3 source data

8) Supplementary Figure 4 source data

9) Supplementary Figure 5 source data

10) Supplementary Figure 6 source data

11) Supplementary Figure 7 source data

12) Supplementary Figure 8 source data

13) Supplementary Figure 9 source data

14) Supplementary Figure 10 source data

15) Supplementary Figure 11 source data

16) Extended Data Figure 2 source data

17) Extended Data Figure 3 source data

18) Extended Data Figure 4 source data

19) Extended Data Figure 5 source data

20) Extended Data Figure 6 source data

21) Extended Data Figure 7 source data

22) Extended Data Figure 8 source data

23) Extended Data Figure 9 source data

24) Extended Data Figure 10 source data


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:

25) Supplementary Video 1 source data

26) Supplementary Video 2 source data

27) Supplementary Video 3 source data

28) Supplementary Video 4 source data

29) Supplementary Video 5 source data

30) Supplementary Video 6 source data

31) Supplementary Video 7 source data

32) Supplementary Video 8 source data

33) Supplementary Video 9 source data

34) Supplementary Video 10 source data

35) Supplementary Video 11 source data

36) Supplementary Video 12 source data

37) Supplementary Video 13 source data

38) Supplementary Video 14 source data

39) Supplementary Video 15 source data

40) Supplementary Video 16 source data


The following contain representative raw data (no processing) for the conditions used in the paper:

41) Representative raw data for rich media, 30C

42) Representative raw data for rich media, 30C with Penicillin G treatment

43) Representative raw data for rich media, 30C with fosfomycin treatment

44) Representative data for rich media, 37C

45) Representative data for minimal media, 30C

46) Representative raw data for minimal media, 37C

47) Representative raw data for rich media, 30C with PC190723 treatment

48) Representative raw data for rich media, 30C with FtsZ(G106S) expression

49) Representative raw data for FtsZ treadmilling in Dhag GFP-FtsZ HT-PBP2B strain

50) Representative raw data for rich media, 30C with 1 mM IPTG

51) Representative raw data for FtsZ treadmilling in rich media, 21C

52) Representative raw data for FtsZ(G106S) treadmilling in rich media, 30C

53) Representative raw data for HT-PBP2B motion horizontally in untreated cells

54) Representative raw data for HT-PBP2B motion in horizontal cells with PC190723 treatment

55) Representative raw data for HT-PBP2B motion in horizontal cells with FtsZ(G106S) expression

56) Representative raw data for HaloTag-FtsW motion in rich media, 30C

Methodological information

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.).

Abbreviations: ROI = Region of Interest.

Instruments used: Bespoke single-molecule fluorescence microscope, Nikon Eclipse Ti, Nikon Eclipse Ti2, and Zeiss Elyra 7 Lattice SIM2.

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).

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).

Extended Data Figures 4 and 6, along with Supplementary Videos 14-16 show data from molecules manually tracked using TrackMate (v7.10.2).

Further data analysis done using Matlab with custom code available on the Whitley lab Github page:

https://github.com/WhitleyLab/Vercini_spt_analysis

The divisome complex was modelled by AlphaFold2, using ColabFold (v1.3.0) and AlphaFold-Multimer (v2).

Date(s) of data collection: 15/12/2021 - 10/12/2023


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FUNDING

Super-resolving the physical mechanisms of bacterial cell division

Wellcome Trust

A single cell, single molecule microscopy platform for antibiotics research

Biotechnology and Biological Sciences Research Council

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