Self-written Code.zip
Contains the self written code used in the analysis for all the figures. It is classified by the program used (FIJI or MATLAB).
For MOCHA-FRAP analysis:
FIJI: FullBarista.ijm for processing the microscope data and obtain the intensities.
MATLAB: MOCHA_FRAP_GUI_v2.m to perform the MOCHA-FRAP normalization steps and calculate the dip (individually and averaged).
For violin plots (MATLAB):
Outlier_removal.m (if required) to find and discard outliers in datasets based on the interquartal distance method.
GMM_analysis_GUI.m to generate the violin plots.
For Pearson correlation coefficient calculation:
FIJI: PCC_preparation.ijm for processing the microscope data and obtain the values of intensities for each pixel.
MATLAB: PCC.m for calculating the Pearson correlation coefficient for each individual cell.

Sequencing files (.gb)
These can be opened using any Molecular biology suite software to see the sequences as well as the features described in each plasmid. A free example of this software is www.benchling.com.
The sequencing was performed externally using illumina.

Analysis files (excel) and analysis files (csv).
Summary of the replicates and collection of the raw data obtained for each experiment, as well as processing (i.e. removing outliers in high-throughput data). In these files, every number that is depicted in graphs in the figures is shown.
A csv version of each excel file tab is given in the file AnalysisFiles(csv).zip file. The name refers to the figure and the tab (i.e. Figure_1-replicates means tab “replicates” in “Figure1” file)

MOCHA-FRAP data folders
Figure 1, Figure 2, Figure 3 and Figure S4 contain half heterochromatin FRAP data (MOCHA-FRAP). This includes the raw files obtained from the Leica microscope (.lif), as well as the regions of interest defined in FIJI and the intensities calculated in these regions of interest using the macro FullBarista.ijm
.lif files opens with FIJI (need BioFormats to open it)
.roi files opens with FIJI (they appear in ROI manager and require an image open to load successfully)

High-throughput raw data folders
The images used to get the intensities and areas that appear in the file Figure 4.xlsx are provided as .tif files and are classified in the immunostaining performed (5mC or H3K9me3), and subdivided into replicates.
.tif files can be open with FIJI

Confocal raw data folders
Figure4_PCC contains 3D confocal data (.lif). To do the analysis, a maximum projection was done for each individual channel and saved as .tif (also provided). The pipeline of analysis is as follows: pre-processing of the data in FIJI using the code PCC_preparation.ijm followed by calculation of the PCC in MATLAB with PCC.m
.lif files opens with FIJI (need BioFormats to open it)
.tif files can be open with FIJI

Simulation and simulation videos
The data of Figure 5 regarding the simulation can be followed in the simulation_description.pdf file. The movies are provided separately in the simulation_videos.zip as mp4 files.