Simultaneous Pathway Activity Inference and Global Gene Expression Analysis Using RNA Sequencing

Data accompanied with the paper "Simultaneous Pathway Activity Inference and Global Gene Expression Analysis Using RNA Sequencing" The data is generated using TF-seq experimental technique that measures binding activity of more than 40 different transcription factors in parallel. It covers three experiments: * Stimulation of wild-type and Myd88 knockout BMDMs with 12 different pathogen associated molecular patterns (PAMPs) * Small molecule screen on BMDMs * Dose-response experiment using Halofuginone on BMDMs, with and without LPS stimulation The data consists of : * fastq files * associated well and reporter tags * counts of all reads, RNA and DNA UMIs * script we used to convert fastq files to count matrices

本数据集配套于论文《使用RNA测序同时实现通路活性推断与全局基因表达分析》（Simultaneous Pathway Activity Inference and Global Gene Expression Analysis Using RNA Sequencing）。该数据集采用TF-seq实验技术生成，可并行检测超过40种转录因子（Transcription Factor, TF）的结合活性。数据集包含三项实验：
* 用12种不同的病原相关分子模式（Pathogen-Associated Molecular Pattern, PAMPs）刺激野生型与Myd88基因敲除的骨髓来源巨噬细胞（Bone Marrow-Derived Macrophage, BMDM，复数为BMDMs）
* 针对骨髓来源巨噬细胞的小分子筛选实验
* 采用常山酮（Halofuginone）对骨髓来源巨噬细胞开展的剂量反应实验，设置脂多糖（Lipopolysaccharide, LPS）刺激与未刺激两组对照
数据集包含以下内容：
* FASTQ文件
* 关联的孔位标签与报告标签
* 所有测序读段（reads）、RNA及DNA的唯一分子标识符（Unique Molecular Identifier, UMI）计数结果
* 用于将FASTQ文件转换为计数矩阵的脚本