Supporting_Information.zip

Supporting Information Summary for: Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells Arnab Sengupta, Greggory M. Rice, and Kevin M. WeeksDepartment of ChemistryUniversity of North Carolina This supporting information contains data and analysis files used in the 16S ribosome RING-MaP paper. The [S1_File] archive contains the following: -- [Analysis_pipeline]: Software programs used to calculate per-nucleotide reactivity rates, and correlation analysis. Files ending in .py can be executed in Python. This folder also contains a README.txt file containing specific details on using the software. Additional .txt files contain example data that can be used to test the programs. The folder named excluded nucleotides contains an indexed list of nucleotides excluded from analysis due to high background mutation. Most of these high background nucleotides are from SNPs in the multiple copies of the ribosomal gene present in E. coli. -- [ArcPlot_CorrelationData_FS2]: RING correlation data and arc-plot diagrams for all treatment conditions and replicates. Treatment conditions are indicated by labels ex (extracted), IC (in-cell), Rif (rifampicin), Spc (spectinomycin), RifSpc (rifampicin and spectinomycin). Replicate information is indicated by numbers 1 and 2. Merged and average replicate data are also included as .txt and .pdf files. ArcPlot diagrams used in Fig. S2 were prepared using these data. -- [Gephi_Data_F2BC_FS3]: Contains network analysis input files. Gephi output files use RING correlation data for network visualization. Files ending in .gephi can be opened in the Gephi software to visualize network diagrams. IC analysis files have information degree analysis and modularity class information under the different treatment conditions. The .svg files contains plots of correlation data superimposed on 16S RNA secondary structure maps. Files with the label "r" contain data for rifampicin treatment, "rs" contain data for rifampicin and spectinomycin treatment. Numerical labels (1-9) represent modularity class. Additional files contain information of nucleotide coloring by network community on the 16S secondary structure. -- [PyMol_Sessions]: Pymol sessions files (.pse) used to prepare Figs. 2C, 3D, 3E, 4A, 4B, 4C, 4D, and 5. Sessions contain defined objects for distinct states and features. Scripts used to create pymol sessions, starting from the pdb file, are also included. The file [S1_Data] contains per-nucleotide DMS reactivity data for conditions including extracted, in-cell, +Rif, and +RifSpc treatment. The file [S2_Data] contains the underlying data used to prepare figures 2A, 3, S2, and S3.

本补充信息总结对应研究：《单分子关联化学探测揭示活细胞内核糖体的大规模结构通信与抗生素大观霉素（spectinomycin）的作用机制》
作者：Arnab Sengupta、Greggory M. Rice、Kevin M. Weeks
单位：北卡罗来纳大学化学系

本补充信息包含16S核糖体RING-MaP论文中使用的实验数据与分析文件。[S1_File]归档包含以下内容：
-- [Analysis_pipeline]：用于计算单核苷酸反应速率并开展关联分析的软件程序。后缀为.py的文件可通过Python运行，该文件夹同时附带README.txt文件，详细说明软件的使用细节。额外的.txt文件为可用于测试程序的示例数据集。名为excluded nucleotides的文件夹收录了因背景突变率过高而被排除在分析之外的核苷酸索引列表，其中多数高背景核苷酸来自大肠杆菌（E. coli）多拷贝核糖体基因的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）。
-- [ArcPlot_CorrelationData_FS2]：涵盖所有处理条件与重复实验的RING关联数据与弧图（arc-plot）。处理条件通过以下标签标识：ex（提取样本）、IC（细胞内样本）、Rif（利福平（rifampicin））、Spc（大观霉素（spectinomycin））、RifSpc（利福平联合大观霉素）；重复实验信息以数字1和2标注。合并后的平均重复数据也以.txt和.pdf文件形式提供。图S2中使用的弧图即基于此类数据生成。
-- [Gephi_Data_F2BC_FS3]：包含网络分析输入文件。Gephi输出文件采用RING关联数据用于网络可视化，后缀为.gephi的文件可通过Gephi软件打开以生成网络图可视化结果。IC分析文件包含不同处理条件下的信息度分析与模块化类别信息。.svg格式文件包含叠加于16S RNA二级结构图谱的关联数据绘图。标签为“r”的文件对应利福平处理组数据，“rs”对应利福平联合大观霉素处理组数据。数字标签（1-9）代表模块化类别。额外文件包含基于16S二级结构按网络群落进行核苷酸着色的相关信息。
-- [PyMol_Sessions]：用于制作图2C、3D、3E、4A、4B、4C、4D及图5的PyMol会话文件（.pse）。会话文件包含针对不同状态与特征的已定义对象，同时附带从pdb（Protein Data Bank）文件出发创建PyMol会话的脚本。

文件[S1_Data]包含提取样本、细胞内样本、+Rif处理组及+RifSpc处理组等条件下的单核苷酸DMS（二甲基硫酸盐，Dimethyl Sulfate）反应活性数据。文件[S2_Data]包含用于制作图2A、图3、图S2及图S3的原始基础数据。