Microscopy-based assessment of H3K27-acetylation at RNA polymerase II clusters during early stages of zebrafish embryo development

This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Marcel Sobucki in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert. To analyse date data, the raw image data are first extracted into MatLab-native files using the MultiPosition_extraction_nd2.m script. The actual analysis is then carried out using first the ClusterAnalysis_Nov2025_part1.m followed by the ClusterAnalysis_Nov2025_part2.m script. Example microscopy images were produced using the ExampleImages.m script. The extracted data can be reviewed using the ReviewExtractedStacks.m script. Additional data needed to be stored in an extra repository due to size limitations: https://doi.org/10.5281/zenodo.8028508本仓库收录了斑马鱼胚胎在合子基因组激活（zygotic genome activation）与原肠胚形成（gastrulation）过程中，RNA聚合酶II（RNA polymerase II）簇处组蛋白3赖氨酸27乙酰化（H3K27ac）分析相关的数据，以及配套的MatLab分析脚本。样本制备与图像采集由马塞尔·索布奇（Marcel Sobucki）在伦纳特·希贝尔（Lennart Hilbert）的实验室完成，图像分析工作则由伦纳特·希贝尔执行。 若需分析数据，原始图像数据需首先通过MultiPosition_extraction_nd2.m脚本提取为MatLab原生格式文件。后续的正式分析需依次运行ClusterAnalysis_Nov2025_part1.m与ClusterAnalysis_Nov2025_part2.m脚本完成。示例显微图像可通过ExampleImages.m脚本生成。提取得到的数据可通过ReviewExtractedStacks.m脚本进行查看与复核。 由于文件尺寸限制，额外所需的数据集需存储于另一仓库：https://doi.org/10.5281/zenodo.8028508