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12 results for “live software”
Experimental package for "Live Software Documentation of Design Pattern Instances"
Experimental package containing the materials and data for an empirical study conducted with the DesignPatterDoc plugin for IntelliJ IDEA.
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (8/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (14/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (7/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (9/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (12/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (11/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (13/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (16/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (10/16)
<p>Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer <em>et al.</em> (2022) ‘<strong>Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics</strong>’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810].</p> <table> <tbody> <tr> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Location</strong></p> </td> </tr> <tr> <td> <p><strong>Centralized GitHub repository</strong> with:</p> <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer <em>et al</em>.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/Keizer-et-al">Keizer <em>et al.</em></a> repository</p> </td> </tr> <tr> <td> <p><strong>Raw microscopy data</strong>:</p> <ul> <li>Experiments performed with the <strong>30’-PR</strong> scheme</li> <li>Experiment performed with the<strong> 100”-PR</strong> scheme</li> <li>Experiment performed with high frame rate (<strong>dt = 0.5”</strong>)</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR)<br> <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR)<br> <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR)<br> <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR)<br> <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5")<br> <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR)</p> </td> </tr> <tr> <td> <p>Concatenated TIFFs and timestamp files for all of the 30’-PR data.</p> </td> <td> <p><a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2)<br> <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2)</p> </td> </tr> <tr> <td> <p><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.</p> </td> <td> <p><a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository</p> </td> </tr> <tr> <td> <ul> <li><strong>Final registered and rotated TIFF files</strong>: <ul> <li><strong>30’-PR</strong> experiments: n = 35 cells</li> <li><strong>100”-PR</strong> experiment, including time projections & kymograph</li> <li><strong>dt = 0.5”</strong> experiments: n = 3 cells</li> <li><strong>no force</strong>: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li><strong>Data files with trajectories and force time profiles</strong> for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510207">Zenodo 13</a></p> </td> </tr> <tr> <td> <p><strong>Single-MNPs fluorescence</strong>: raw data, Python/Fiji scripts and instructions</p> </td> <td> <p><a href="https://zenodo.org/record/6510209">Zenodo 14</a></p> </td> </tr> <tr> <td> <ul> <li>MagSim, <strong>Python library for magnetic simulations</strong></li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <p><a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository</p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 1</strong>: Gradient of free GFP-ferritin in solution</p> <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/4627062">Zenodo 15</a></p> </td> </tr> <tr> <td> <p><strong>Force calibration – Method 2</strong>: Attraction of ferritin-coated beads (Fig. S7)</p> <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <p><a href="https://zenodo.org/record/6510211">Zenodo 16</a></p> </td> </tr> <tr> <td> <ul> <li><strong>Python library for force inference</strong> using different polymer models</li> </ul> </td> <td> <p><a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository</p> </td> </tr> </tbody> </table> <p><strong>License:</strong> All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646"><em>Author Accepted Manuscript</em></a> of the study [Keizer <em>et al.</em> 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810"><em>Final Published Version</em></a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).</p> <p> </p> <p><strong>Overview of the raw data repositories (Zenodo 1-10)</strong></p> <p><em>Refer to the Material and Methods section of the article for details on data production.</em></p> <p>Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains:</p> <ul> <li>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: <ul> <li>The various positions were imaged before injection (folder with the <em>_preInjection,</em> <em>_1-pre-inj or _1-inj_1</em> suffix)</li> <li>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>)</li> <li>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>)</li> <li>They were then imaged after the magnet was removed (suffix <em>_release1</em>)</li> <li>Finally, the cells were monitored after the experiment (suffix <em>_after-exp</em> or <em>_postexp</em>)</li> </ul> </li> <li>A text file named <em>lab_journal_[...].txt</em> contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul> <p> </p> <p><strong>Overview of the concatenated datasets (Zenodo 11-12)</strong></p> <p>In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains:</p> <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li><strong>path</strong> (Relative path): Reference to the original (raw MicroManager) file</li> <li><strong>start_time</strong> (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li><strong>time_in_file</strong> (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li><strong>start_time_s</strong> (seconds): Variable start_time converted to a number of seconds</li> <li><strong>time</strong> (seconds): Sum of start_time and time_in_file</li> <li><strong>timestamp</strong> (Timestamp): Variable time, back-converted to a timestamp</li> <li><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</li> <li><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</li> <li><strong>forceActivated</strong> (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li><strong>seconds_since_first_magnet_ON</strong> (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li><strong>Frame</strong> (Integer) Frame number (1-indexed)</li> <li><strong>Positions</strong> (Integer): The position number</li> </ul> </li> </ul> <p> </p> <p><strong>Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16)</strong></p> <p>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.</p>
Clinical Investigation Evaluating the Use of NETSmart Solution , Incorporated to NETSoins Software, in the Care and Support of Elderly People Living in Nursing Homes
ClinicalTrials.gov study NCT07027358. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics'" – Data, software and documentation (main github repository)
<p>Files that will be uploaded to <a href="https://github.com/CoulonLab/Keizer-et-al">https://github.com/CoulonLab/Keizer-et-al</a> upon acceptance.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.