A physical model of transcription factor dynamics through human chromosomes: data and code

This record contains the data and analysis code supporting the manuscript:“3D genome architecture regulates the traffic of transcription factors throughout human chromosomes.”

The repository includes curated, post-aggregation outputs from an in-silico model to simulate the dynamics of a specific transcription factor protein through 3D architecture of a specific human chromosme. We have also included analysis scripts and documentation required to reproduce the reported results and figures. The repository contains sample trajectory files containing list of x, y, z positions of all TF molecules from all timepoints of a demo simulation, and all the pooled datasets containing TF residence times on binding sites, all the hopping spatial and genomic distance of the TFs from all our simulations.

A demo simulation and analysis code are provided, including python classes that are used to create the polymer model of chromosomes. The binding sites locations, extracted from ChIPseq data of the TF on the given chromosome, are overlayed on the polymer. All the ChIPseq analysis codes and resultant location data of binding sites are also included. 

Raw molecular dynamics trajectories and intermediate per-trajectory analysis files (multiple terabytes) are not included due to their size. The repository instead provides final processed datasets and matlab scripts sufficient to reproduce all figures.

Input chromatin structures were generated using a previously published ensembe (Cheng et al eLife 9, e60312 (2020)). A small subset of representative structures is included for inspection. The full ensemble is not redistributed here and is available at: https://ndb.rice.edu. 

Processed datasets are also available as a downloadable archive; see repository README for directory structure and file descriptions.

本数据集包含支撑研究论文《3D基因组架构调控转录因子在人类全染色体中的动态转运》的实验数据与分析代码。

本代码仓库包含经整理的聚合后计算机仿真模型输出结果，该模型用于模拟特定转录因子（Transcription Factor, TF）蛋白在特定人类染色体3D架构中的动态行为。此外，我们还提供了复现论文中报道结果与图表所需的分析脚本与配套文档。仓库内包含演示仿真全时间步下所有TF分子x、y、z坐标列表的示例轨迹文件，以及涵盖所有仿真实验的TF结合位点驻留时间、TF跳跃行为的空间与基因组距离的整合数据集。

本仓库提供演示仿真与分析代码，包括用于构建染色体聚合物模型的Python类。从给定染色体上该TF的染色质免疫共沉淀测序（ChIP-seq）数据中提取的结合位点坐标，已叠加至聚合物模型中。同时附带所有ChIP-seq分析代码与结合位点定位结果数据。

由于文件体量过大（达数太字节），原始分子动力学轨迹文件与单轨迹中间分析文件未纳入本仓库。本仓库仅提供可复现所有图表的最终处理后数据集与Matlab脚本。

输入的染色质结构基于已发表的集成结构集生成（Cheng等人, eLife 9, e60312, 2020）。本仓库仅包含少量代表性结构用于预览查看，完整集成结构集未在此处分发，可通过以下链接获取：https://ndb.rice.edu。

处理后的数据集也可通过下载归档包获取；有关目录结构与文件说明，请参阅仓库README文档。