Supporting Data for "ZC3H8 regulates rDNA transcription by suppression of R loop formation"

<b>Project Overview:</b>This project investigates the role of ZC3H8, a nucleolar protein, in safeguarding genomic integrity during ribosome biogenesis. The nucleolus, as the site of ribosomal RNA (rRNA) synthesis, is one of the most transcriptionally active regions in the cell and is particularly vulnerable to genomic instability. Ribosomal DNA (rDNA), which resides in the nucleolus, is prone to the formation of R loops—three-stranded nucleic acid structures that can interfere with transcription, thereby threatening genome stability.The study demonstrates that ZC3H8 may play a critical role in suppressing R loop formation at rDNA loci. Mechanistically, ZC3H8 functions in concert with DHX9, an RNA helicase known to resolve R loops. ZC3H8 binds preferentially to single-stranded RNA, and this interaction is proposed to stabilize the RNA strand during DHX9-mediated unwinding of R loops. This cooperative mechanism supports efficient rRNA synthesis while preserving the structural and functional integrity of the rDNA.<b>Dataset Contents:</b>The dataset includes raw and processed experimental data organized by thesis chapters and figures. Data formats include high-resolution immunofluorescence images, Western blot scans, quantification files, RNA-seq datasets, and schematic illustrations. All files are arranged to mirror the thesis structure, ensuring clear correspondence between data and manuscript figures.<br><b>Key Directories and File Types:</b><b>Chapter 1 – Introduction (Figures 1.1–1.2):</b>Adobe Illustrator (.ai) schematics illustrating rDNA structure and nucleolar functions.<b>Chapter 3 – Experimental Results (Figures 3.1–3.13):</b><b>Raw Data:</b>Immunofluorescence images (.tif, .rar)Western blot scans (Image Lab format)RNA-seq analysis files (.csv, .xlsx, .txt)EMSA gel imagesQuantification data (.pzfx, .pzf) from GraphPad PrismProtein structure prediction outputs (AlphaFold, PyMOL)<b>Organised Data:</b>Finalized figure panels (.tif)Schematics (.ai) and processed visualizations used directly in the thesis manuscript.<br><b>Software and Equipment Used:</b>Image Analysis: Fiji (ImageJ v1.53f51)Quantitative Analysis: GraphPad Prism (v7.0 or higher)Microscopy: Zeiss LSM 780 confocal microscope<br><b>Intended Use:</b>The dataset supports reproducibility and transparency of the thesis findings. It is intended for researchers interested in rDNA transcription, nucleolar biology, RNA processing, and protein–nucleic acid interactions. The detailed file organization facilitates targeted reuse of specific data elements (e.g., IF quantifications, RNA-seq processing).

项目概述：
本项目探究核仁蛋白ZC3H8在核糖体生物发生过程中维护基因组完整性的作用。核仁（nucleolus）作为核糖体RNA（ribosomal RNA, rRNA）的合成场所，是细胞中转录活性最高的区域之一，且极易发生基因组不稳定。位于核仁内的核糖体DNA（ribosomal DNA, rDNA）易于形成R环——一种可干扰转录、进而威胁基因组稳定性的三链核酸结构。本研究证实，ZC3H8可在rDNA位点发挥抑制R环形成的关键作用。机制层面，ZC3H8与已知可解离R环的RNA解旋酶（RNA helicase）DHX9协同行使功能。ZC3H8优先结合单链RNA，该相互作用被认为可在DHX9介导的R环解旋过程中稳定RNA链。这种协同机制在保障高效rRNA合成的同时，维持了rDNA的结构与功能完整性。

数据集内容：
本数据集包含按学位论文章节与图表分类整理的原始及经处理的实验数据。数据格式涵盖高分辨率免疫荧光图像、蛋白质免疫印迹（Western blot）扫描结果、定量文件、RNA测序（RNA-seq）数据集及示意图。所有文件均依照论文结构排布，确保数据与手稿图表一一对应。

关键目录与文件类型：
第一章——绪论（图1.1~1.2）：包含用于阐释rDNA结构与核仁功能的Adobe Illustrator（.ai）格式示意图。
第三章——实验结果（图3.1~3.13）：
原始数据：免疫荧光图像（.tif、.rar）、蛋白质免疫印迹扫描结果（Image Lab格式）、RNA-seq分析文件（.csv、.xlsx、.txt）、电泳迁移率变动分析（electrophoretic mobility shift assay, EMSA）凝胶图像、GraphPad Prism导出的定量数据（.pzfx、.pzf）、蛋白质结构预测结果（AlphaFold、PyMOL格式）
整理后数据：用于学位论文的最终定稿图版（.tif）、示意图（.ai）及直接用于论文手稿的经过处理的可视化素材。

所用软件与设备：
图像分析：Fiji（ImageJ v1.53f51）
定量分析：GraphPad Prism（v7.0及更高版本）
显微镜成像：Zeiss LSM 780共聚焦显微镜

预期用途：
本数据集旨在支撑本学位论文研究结果的可重复性与研究透明度，可供关注rDNA转录、核仁生物学、RNA加工及蛋白质-核酸相互作用的科研人员使用。其精细化的文件排布便于研究者针对性复用特定数据元素（如免疫荧光定量结果、RNA-seq处理数据）。