Microscopy-based assessment of RNA polymerase II clusters and H3K27ac level during differentiation of cultured mouse embryonic stem cells

This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters and H3K27ac levels over the course of differentiation of cultured mouse embryonic stem cells (mESCs). The cells were induced towards differentiation by RHB-A culture treatment. The treatment was carried out in duplicate in independent experiments. Time course data were obtained by collection of cells at 6, 12, 24, 48, and 72 hours following the beginning of induction. Control data from unindexed cells were obtained at 6, 12, and 24 hours. Cells were cultured, treated, collected, and fixed at University Medical Center Göttingen by Matthias Akyel and Carmelo Ferrai. Fixed cells were fluorescently labeled and microscopy images were recorded and analyzed at Karlsruhe Institute of Technology by Alica Schmidt-Heydt, Yuzhi Bao, Alicia Günthel, and Lennart Hilbert. The image analysis was carried out by Lennart Hilbert and Stephan Allgeier at Karlsruhe Institute of Technology. To analyse data, the raw image data were extracted and processed in batches. The underlying set of MatLab, bash, and slurm scripts are provided within this repository. The raw data are too extensive to store in Zenodo repositories. Within this repository, we provide the derived analysis results, which were obtained by processing on the Large Scale Data Facility as well as the bwUniCluster of Karlsruhe Institute of Technology. These derived analysis results are contained in the file AfterObjectAnalysis_combined_v7.mat provided within this repository.The final analysis steps were carried out locally, using the MatLab script ClusterAnalysis_mESC_Oct2025_part2.m.