Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing

Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.

Zhang, Annie, Massachusetts Institute of Technology, ORCID: 0000-0003-3939-2585

DOI: 10.5281/zenodo.7814499

Primary publication DOI: https://doi.org/10.1073/pnas.2305556120

Folder Structure

Source data are organized based on the parent figures from the main text (Figs 1-6). Source data from supplementary figures associated are placed within the associated parent figure folder. All figures, their associated parent figures, and the experiment names from which these figures are derived are summarized in the 'Summary.xlsx' file.

File Formats

1. Integrated trace files are saved as .dat files.

- These trace files are obtained by integrating the fluorescence intensity contained within each DNA spot, or Area of Interest (AOI), over the range of the experimental time frame. They can be read and viewed in Matlab or the Matlab program imscroll, which is publicly available: https://github.com/gelles-brandeis/CoSMoS_Analysis.

- Naming of files:

The experiment name is specified at the beginning of the file name.

The excitation and emission fields are specified using the following abbreviations.

Gex: Green excited (Donor excited)

Rex: Red excited (Acceptor excited)

GexRex: Green and red excited (Donor and acceptor excited)

Gem: Green emission (Donor emission)

Rem: Red emission (Acceptor emission)

To read the .dat integrated trace files in Matlab the user may type: 

>>[fn fp] = uigetfile

% use the dialog box to mouse click on the appropriate *.dat file, then type:

>>eval(['load ' [fp fn] ' -mat'])

% This loads an aoifits structure array into the Matlab command environment

The integrated trace data is stored in the aoifits.data matrix. A description of the columns is in the aoifits.dataDescription.

The first five columns within aoifits.data are the most relevant to view fluorescence emission intensities at individual AOIs over time.

Column 1: aoinumber

Column 2: framenumber

Column 3: amplitude (of fluorescence emission)

Column 4: xcenter of the aoi

Column 5: ycenter of the aoi

2. Time Intervals are stored as excel spreadsheet (.xlsx) files.

These files contain the AOI numbers used for analysis and frame numbers that correspond to specific events, such as protein arrival and departure events.

3. For experiments with EFRET analysis performed, EFRET values are stored as .mat matrix files.

Column 1: Time in seconds after protein colocalization with DNA

Column 2: EFRET values

Column 3: AOI number

Column 4: Frame number