Data supporting the paper "The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of the osmoregulated proVWX operon in Escherichia coli"

doi:10.4121/21065275.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: 10.4121/21065275
Datacite citation style:
Remus T. Dame; Crémazy, Frédéric; Hofmann, Andreas; Rashid, Fatema Zahra; Grainger, David et. al. (2023): Data supporting the paper "The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of the osmoregulated proVWX operon in Escherichia coli". Version 1. 4TU.ResearchData. dataset. https://doi.org/10.4121/21065275.v1
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite
Dataset

This is data supporting the paper titled, "The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of the osmoregulated proVWX operon in Escherichia coli"


It consists of:

 - NGS data of Hi-C libraries prepared for Escherichia coli showing the importance of methanol treatment prior to formaldehyde fixation, and of performing proximity ligation on the insoluble fraction of fixed, digested chromatin for increasing the signal-to-noise ratio of chromosome contact maps

 - NGS data of Hi-C libraries prepared for Escherichia coli growing exponentially in low salt LB medium (0.08 M NaCl), and high salt LB (0.3 M NaCl), and of E. coli at exponential phase in low-salt LB medium (0.08 M NaCl) subjected to a hyperosmotic shock (from 0.08 M NaCl to 0.3 M NaCl) for 10 minutes. The data shows that the chromosome of E. coli undergoes global and local chromosome remodelling in response to osmolarity

 - Raw data files of RT-qPCR experiments of the proVWX operon and its flanking regions performed in MG1655 ΔendA (NT331), MG1655 ΔendA carrying a mutated proVWX regulatory region (NT644), NT331 ΔstpA, and NT331 Δrnc

 - Raw data files of 3C-qPCR experiments of the proVWX operon and its flanking regions performed using the σ70 transcription start site fragment (referred to as the proU3_NlaIII fragment in our studies) as the anchor fragment in NT331, NT644, and NT331 treated with rifampicin.


history
  • 2023-09-26 first online, published, posted
publisher
4TU.ResearchData
format
*.hic files that can be opened with Juicebox (https://github.com/aidenlab/Juicebox/wiki/Download); *.seq files that can be opened using Chromas (http://technelysium.com.au); *.fastq files *.pdf, *.xlsx, and *.csv files.
funding
  • VICI 016.160.613/533
  • Resolving the fundamental building principles of the genome (grant code OCENW.GROOT.2019.012) [more info...] Dutch Research Council
  • HFSP RGP0014/2014
organizations
Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University
Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay
Statistical Physics and Theoretical Biophysics, Heidelberg University
School of Biosciences, University of Birmingham

DATA

files (3)