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

This is data supporting the paper titled, "The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of the osmoregulated <em>proVWX</em> operon in <em>Escherichia coli</em>"<br>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 <em>Escherichia coli</em> growing exponentially in low salt LB medium (0.08 M NaCl), and high salt LB (0.3 M NaCl), and of <em>E. coli</em> 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 <em>E. coli</em> undergoes global and local chromosome remodelling in response to osmolarity - Raw data files of RT-qPCR experiments of the <em>proVWX</em> operon and its flanking regions performed in MG1655 ΔendA (NT331), MG1655 Δ<em>endA</em> carrying a mutated <em>proVWX</em> regulatory region (NT644), NT331 Δ<em>stpA</em>, and NT331 Δ<em>rnc</em> - Raw data files of 3C-qPCR experiments of the <em>proVWX</em> 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.<br>

本数据集用于支撑题为"大肠杆菌（Escherichia coli）中渗透调控的<em>proVWX</em>操纵子的局部三维染色质组织与转录之间的环境调控相互作用》的研究论文。数据集包含以下内容：<br>• 针对大肠杆菌（Escherichia coli）构建的Hi-C文库的下一代测序（Next Generation Sequencing，NGS）数据，该数据证实了在甲醛固定前进行甲醇处理、以及在固定并酶解的染色质不溶组分中开展邻近连接实验对提升染色体接触图谱信噪比的重要性。<br>• 分别针对在低盐LB培养基（0.08 M NaCl）、高盐LB培养基（0.3 M NaCl）中指数生长期的大肠杆菌（Escherichia coli）构建的Hi-C文库的NGS数据，以及在低盐LB培养基（0.08 M NaCl）中处于指数生长期、经10分钟高渗冲击（从0.08 M NaCl至0.3 M NaCl）的大肠杆菌（E. coli）构建的Hi-C文库的NGS数据。该数据表明，大肠杆菌的染色体会响应渗透压变化发生全局及局部染色质重塑。<br>• 针对<em>proVWX</em>操纵子及其侧翼区域开展的实时定量PCR（Real-Time Quantitative PCR，RT-qPCR）实验原始数据文件，实验分别在MG1655 ΔendA（NT331）、携带突变型<em>proVWX</em>调控区的MG1655 ΔendA（NT644）、NT331 ΔstpA以及NT331 Δrnc菌株中完成。<br>• 针对<em>proVWX</em>操纵子及其侧翼区域开展的3C-qPCR实验原始数据文件，实验以σ70转录起始位点片段（本研究中称为proU3_NlaIII 片段）作为锚定片段，分别在NT331、NT644以及经利福平处理的NT331菌株中完成。