DOI: 10.5281/zenodo.6510107
title: Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (11/16)

description: Data, software and documentation to reproduce the results presented in [Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605, DOI: 10.1126/science.abi9810]. <strong>Description</strong> <strong>Location</strong> <strong>Centralized GitHub repository</strong> with: Local copy of all the code and trajectory/force files Jupyter notebooks to make all the graphs in Keizer <em>et al</em>. Pointers to all the datasets also shown in this table Keizer <em>et al.</em> repository <strong>Raw microscopy data</strong>: Experiments performed with the <strong>30’-PR</strong> scheme Experiment performed with the<strong> 100”-PR</strong> scheme Experiment performed with high frame rate (<strong>dt = 0.5”</strong>) Zenodo 1 (30’-PR)<br> Zenodo 2 (30’-PR)<br> Zenodo 3 (30’-PR)<br> Zenodo 4 (30’-PR)<br> Zenodo 5 (30’-PR)<br> Zenodo 6 (100”-PR)<br> Zenodo 7 (30’-PR)<br> Zenodo 8 (30’-PR)<br> Zenodo 9 (dt = 0.5")<br> Zenodo 10 (30’-PR) Concatenated TIFFs and timestamp files for all of the 30’-PR data. Zenodo 11 (1/2)<br> Zenodo 12 (2/2) <strong>Python pipeline </strong>to generate (i) concatenated movies, (ii) cropped and rotated movies for each cell, and (iii) force time profiles for each cell. ChroMag-pipeline repository <strong>Final registered and rotated TIFF files</strong>: <strong>30’-PR</strong> experiments: n = 35 cells <strong>100”-PR</strong> experiment, including time projections & kymograph <strong>dt = 0.5”</strong> experiments: n = 3 cells <strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation <strong>Data files with trajectories and force time profiles</strong> for all analyzed cells Instructions and Fiji/Python scripts to reproduce these files. Zenodo 13 <strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions Zenodo 14 MagSim, <strong>Python library for magnetic simulations</strong> Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6). MagSim repository <strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution Raw microscopy data (6 pillars; Fig. S6B-C) Calculated force maps, with Fiji scripts and instructions to generate them. Zenodo 15 <strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7) Raw microscopy data (free diffusion and attraction) Python/Fiji scripts to calculate forces. Zenodo 16 <strong>Python library for force inference</strong> using different polymer models rouselib repository <strong>License:</strong> All the code, data and documentation in this repository is under GPLv3 license. The <em>Author Accepted Manuscript</em> of the study [Keizer <em>et al.</em> 2022] is under CC-BY 4.0 license. The <em>Final Published Version</em>, published by AAAS, is not (more information). <strong>Overview of the raw data repositories (Zenodo 1-10)</strong> <em>Refer to the Material and Methods section of the article for details on data production.</em> Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains: The raw MicroManager folder architecture (one folder contains multiple positions on the coverslip). On occasions where placement or removal of the external magnet led to a loss of focus, the acquisition was stopped and restarted, creating a new MicroManager folder each time. For instance: The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix) These positions were imaged again after injection (suffix <em>_postInjection,</em> <em>_2-post-inj </em>or <em>_1-inj_2</em>) and before the magnet was added (suffix <em>_beforeexp</em> or <em>_before-attr</em>) They were imaged again with the magnet added (suffix <em>_attraction1</em>). If acquisition was stopped and restarted an extra folder is created (suffix <em>_attraction2</em>) They were then imaged after the magnet was removed (suffix <em>_release1</em>) Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>) A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure Note: the MicroManager metadata in the TIFF file are fully populated <strong>Overview of the concatenated datasets (Zenodo 11-12)</strong> In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the ChroMag-pipeline repository. The folder contains: One TIFF file per selected position One .xls file per selected position, with one line per frame, and columns with the following information: <strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file <strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed). <strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint <strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds <strong>time</strong> (seconds): Sum of start_time and time_in_file <strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp <strong>timeOn</strong> (Timestamp): Time(s) when the magnet was added. This timestamp is provided in the datasets.cfg file in the github repository chromag-pipeline <strong>timeOff</strong> (Timestamp): Time(s) when the magnet was removed. This timestamp is provided in the datasets.cfg file in the github repository chromag-pipeline <strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff) <strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time. <strong>Frame</strong> (Integer) Frame number (1-indexed) <strong>Positions</strong> (Integer): The position number <strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong> These datasets and their analysis are fully described in the <em>Materials and Methods</em> section of the article and in the different README.md files within the various folders of the datasets.
description: This work received funding from: • the LabEx CELL(N)SCALE (ANR-11-LABX-0038, ANR-10-IDEX-0001-02) (MD, DF, AC) • the Agence Nationale de la Recherche (project CHROMAG, ANR-18-CE12-0023-01) (MD, AC), • the PRESTIGE program of Campus France (PRESTIGE-2018-1-0023) (VK) • the ATIP-Avenir program of CNRS and INERM, the Plan Cancer of the French ministry for research and health (AC, DF), • the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 757956) (AC), • the LabEx DEEP (ANR-11-LABX-0044, ANR-10-IDEX-0001-02) (AC), • the program Fondation ARC (grant agreement PJA 20161204869) (AC) • the Institut Curie (DF, AC) • the Centre National de la Recherche Scientifique (CNRS) (AC, DF) • the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 666003 (SH) • the NIH GM114190 grant (LAM), • the MIT-France Seed Fund (LAM, MD), • LAM is a recipient of Chaire Blaise Pascal by Île-de-France Administration (LAM).