Simulation code accompanying the publication "Cohesin supercoils DNA during loop extrusion"

doi:10.4121/f60f272e-c66a-4755-942d-6de6f62a10ed.v1
The doi above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
doi: 10.4121/f60f272e-c66a-4755-942d-6de6f62a10ed
Datacite citation style:
Barth, Roman (2024): Simulation code accompanying the publication "Cohesin supercoils DNA during loop extrusion". Version 1. 4TU.ResearchData. software. https://doi.org/10.4121/f60f272e-c66a-4755-942d-6de6f62a10ed.v1
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite
Software

Research objective: computationally determine the linking number of plasmids after SMC-mediated DNA loop extrusion with twist and topoisomerase-mediated Lk change

Type of research: Comparison of computational model to experimental bulk plasmid assays

Method of data collection: 1D Monte Carlo simulations

Type of data: custom python code (.py) and .json data file

history
  • 2024-01-26 first online, published, posted
publisher
4TU.ResearchData
format
python code (.py) and .json data file
funding
  • ERC Advanced Grant LoopingDNA (no. 883684)
  • NWO grant OCENW.GROOT.2019.012 (grant code OCENW.GROOT.2019.012) NWO
  • NanoFront
  • BaSyC - Building a Synthetic Cell (grant code 024.003.019) [more info...] Dutch Research Council
  • Boehringer Ingelheim
  • Austrian Research Promotion Agency Headquarter grant FFG-852936 (grant code FFG-852936 ) Austrian Research Promotion Agency Headquarter
  • European Research Council under the European Union’s Horizon 2020 research and innovation programme GA No 101020558 (grant code 101020558) European Research Council under the European Union’s Horizon 2020 research and innovation programme
  • Human Frontier Science Program RGP0057/2018 (grant code RGP0057/2018))
  • Vienna Science and Technology Fund (grant LS19-029) (grant code LS19-029) Vienna Science and Technology Fund
organizations
TU Delft, Faculty of Applied Sciences, Kavli Institute of Nanoscience Delft, Department of Bionanoscience, Cees Dekker group;
Research Institute of Molecular Pathology (IMP), Vienna, Jan-Michael Peters group

DATA

files (3)