Daftar Isi: Association of oligopaint FISH labeled super-enhancers and genes with polymerase clusters

Daftar Isi:

This data set assesses the placement of different genomic regions relative to clusters formed by RNA polymerase II in zebrafish embryos. RNA polymerase was labeled by immunofluorescence, genomic regions by oligopaint DNA fluorescence in-situ hybridization (FISH). Microscopy images were acquired by instant-SIM microscopy, and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.
To analyze the extracted image, run the script OligoPaint_PairAnalysis.m (In the beginning of the script, you can choose the file path to the data extracted under point. Make sure the extracted files are ordered as indicated by the script, so the script can locate the files) In case you would like to analyze from the raw data obtained from the microscope, you will first need to download the three raw data files (SE1-SE6, SE7-SE12, genes, links provided in the study). Then install bfmatlab from OME, add it to the MatLab path. Lastly, extract the image data by running the script MultiPosition_extraction_nd2.m (The script must be run twice, once with the genesFlag variable in the beginning of the script set to true, once with the genesFlag set to false. Also make sure the downloaded image data are placed at the right file locations.)