Fig. 6 | Tracking mitochondria in ALS motor axons

<p dir="ltr">This item is part of the <b>Figshare Project</b>:<br><b>Early mitochondrial dysfunction revealed across FUS- and TARDBP-ALS at single cell resolution</b></p><p><br></p><p dir="ltr">From <i>Data Availability Statement</i> for the paper in <i>Nature Communications</i> entitled:</p><p dir="ltr"><b>Single-cell RNA sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS</b></p><p dir="ltr">"We have deposited all raw and processed RNA sequencing data generated in this study on the NCBI Gene Expression Omnibus (GEO) under the accession number GSE226482. The <i>C9orf72</i>-ALS bulk RNA sequencing data was retrieved directly from the authors of the study.</p><p dir="ltr">[Items under this Figshare Project contain:] "Scans of fluorescent western blots, raw imaging files from confocal microscopy, the analysis files from Opera Phenix, qPCR data sets, and Seahorse assay result files."</p><p>--------------------------------------------</p><p dir="ltr">[Item specific description:]</p><p dir="ltr">Motor neurons were generated from iPSC by differentation according to Nijssen et al, 2019. BioProtocol (PMID: 33654821). Embryoid bodies containing motor neuron progenitors were attached whole at day 9, followed by maturation during which axons grow radially outward.</p><p dir="ltr">From day 27 onwards and as indicated, mitochondria were labelled with TMRM for 30 min prior to live cell imaging to record time-lapses.</p><p dir="ltr">These files are images and time-lapse videos of mitochondrial movement in iPSC-derived motor axons based on TMRM-stained mitochondria. The file format is .czi, through the ZEN software (Zeiss). Zeiss recommends using ImageJ and the ImageJ-based <a href="https://imagej.net/software/fiji/" rel="noreferrer" target="_blank">Fiji software package</a>.</p><p dir="ltr">For analysis of mitochondrial movement, individual mitochondria were traced in Fiji using the TrackMate 7 extension with the StarDist detector and a Sparse LAP tracker (as in ‘mitotracker.py’). The mitochondrial traces were then annotated and analysed in R (version 4.2.0) using our custom package ‘mitotrackR’ (<a href="https://github.com/schwi24/mitotrackR" target="_blank">https://github.com/schwi24/mitotrackR</a>).</p><p dir="ltr">Information about the microscopy file format CZI can be found here: https://www.zeiss.com/microscopy/en/products/software/zeiss-zen/czi-image-file-format.html</p>