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