Microscopy-based measurements of p62 recruitment in HeLa
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Microscopy-based pUb-coverage measurements of mitochondria in iNeurons
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell lines
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Immunocytochemical analysis
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Evaluation of pUb kinetics using 3D-SIM
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Cell culture, transfection, and imaging
By savannah onThis protocol details the general preparation of cells for imaging and also for imaging experiments involving cellular hypotonic shock and cytosolic Ca2+ changes as they were performed in https://doi.org/10.1083/jcb.202010004.
Cell culture, transfection, and imaging
By savannah onThis protocol describes general procedures for culturing HeLa cells, transient transfection, and imaging using an Andor Dragonfly spinning disk confocal system.
Protocol collection for “PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems”
By savannah onCollection of protocols associated with preprint (https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1.full). Protocols: Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell lines Microscopy-based pUb-coverage measurements of mitochondria in iNeurons Microscopy-based measurements of p62 recruitment in HeLa Microscopy-based mtDNA turnover measurements in HeLa and iNeurons Microscopy-based mitochondrial morphology measurements in iNeurons
Flow cytometry-based measurement of mitophagic flux
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
Evaluation of mtKeima foci in induced neurons (iNeurons)
By savannah onAssociated with preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
LC3-lipidation-assay
By savannah onProtocol for an in vitro LC3 lipidation assay using purified proteins and synthetic liposomes.
NHS-ester-protein-labeling
By savannah onProtocol for labeling a purified protein with an NHS ester fluorescent dye.
Evaluating endocytic rate in cells
By savannah onAssess endocytic rate in cells using tagged transferrin (Alexa647) and flow cytometry readout.
Fluorescently labeled polyamine uptake (via Flow Cytometry)
By savannah onAssess polyamine uptake capacities of a specific cell line after incubation with fluorescently labeled polyamines and mean fluorescence intensity acquisition via flow cytometry. Watch an interview about this protocol with Mujahid Azfar, MSc.
Creating pooled CRISPR-Cas9 knock-outs in NIH-3T3 cells
By savannah onTo validate a genome wide CRISPR screen, the authors select the top hits and create lentiviruses to validate the hits. Rather than screening each virus from single cell clones, the authors analyze the infected cells as pools according to this protocol.
CRISPR-Cas9 screen in NIH-3T3 cells to identify modulators of LRRK2 function
By savannah onThis protocol describes a pooled, CRISPR Cas9 screen to identify modulators of LRRK2 activity. The CRISPR-Cas9 based screen is carried out in mouse cells using a ready-to-use pooled guide RNA (gRNA) mouse library consisting of 78,637 gRNAs targeting 19,674 genes and an extra 1,000 control gRNAs.
In Silico analysis links the NSL complex to Parkinson’s disease and the mitochondria – protein-protein interaction data to functional enrichment analysis
By savannah onThis bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to Parkinson’s disease progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE, and MIST, for curated, literature-derived protein-protein interaction (PPI) data.
Untargeted lipidomics analysis for Golgi immunopurification (Golgi-IP)
By savannah onThis protocol provides details for analyzing GolgiIP lipidomics samples using liquid chromatography mass spectrometry (LC-MS) for nonpolar lipid profiling.
Golgi immunopurification (Golgi-IP) for subcellular lipid profiling
By savannah onThis protocol provides details for preparing Golgi-IP lipidomics samples.
Untargeted metabolomics analysis for Golgi immunopurification (Golgi-IP)
By savannah onThis protocol provides details for analyzing GolgiIP metabolomics samples using liquid chromatography mass spectrometry (LC-MS) for polar metabolite profiling.
