Immunocytochemistry of autophagosome-associated proteins
By onProtocol for immunocytochemistry used on primary cortical neurons in Palumbos et al., 2025. Protocol can be adapted to other cultured cell types and antibodies. Described protocol works for autophagosome associtated proteins
Protein Extraction, Mass Spectrometry, and Data Analysis
By onProtocol describing protocol of protein extraction, mass spectrometry, and subsequent data analysis for Palumbos et al., 2025. All steps of the protocol were performed by CHOP PENN Proteomics core.
CalceinAM labeling of Extracellular Vesicles
By onProtocol used to visualize intact vesicles isolated from primary murine neurons. Protocol used in Palumbos et al., 2025 and adapted from https://doi.org/10.1371/journal.pone.0317689
Apoptosis Detection with CellEvent Caspase-3/7
By onApproach combines CellEvent Caspase 3/7 reporter with Cellpose machine learning detection. Expanded methods applying these two approaches individually are available (see Invitrogen directions and Stinger and Pachitariu 2025).
Protocols for Jaidar et al., 2025 “Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning”
By onProtocol outlines steps for making guide cannulas, viral injections, and inserting cannulas in 5-week-old mice. Detailed behavioral protocol included for long-term two-photon imaging studies.
ATG9A-vesicle isolation protocol_
By onHap1 cells were previously CRISPR engineered in our lab to contain ATG9A endogenously tagged on the C-terminus with mEGFP-3C-FLAG.
Co-immunoprecipitation ER-phagy receptors
By onThis protocol details the co-immunoprecipitation of ER-phagy receptors.
Autophagy detection assay
By onAutophagosome detection using Dojindo DAPRed dye and Lysotracker Green in neurons
Protocol for CRISPR-based manipulation and visualization of endogenous α-synuclein in cultured mouse hippocampal neurons
By onProtocol for depleting or tagging endogenous α-syn using virally-delivered CRISPR-Cas9 in hippocampal neurons
Mitophagy detection assay
By onDetection of mitophagy flux in neurons using Dojindo Mtphagy dye and Lysotracker Green
Assay for lysosomal activity using Magic Red
By onAssay for lysosomal Cathepsin B activity in neurons using Magic Red
Immunoprecipitation from primary neurons
By onProtocol for immunoprecipitating proteins from neuronal lysates
all protocols related to ‘Loss of the lysosomal lipid flippase ATP10B leads to progressive dopaminergic neurodegeneration and Parkinsonian motor deficits’
By onall protocols related to 'Loss of the lysosomal lipid flippase ATP10B leads to progressive dopaminergic neurodegeneration and Parkinsonian motor deficits
Choice Reaction Time Reaching Task for Non-human Primate
By onThis protocol describes the behavioral task used with both healthy and MPTP-induced hemiparkinsonian non-human primates in the Turner Lab at the University of Pittsburgh, as well as the training procedure for introducing the task to naïve NHPs.
