Immunohistochemistry Protocol – Ford Lab
By onThis protocol describes the steps for performing immunohistochemistry.
Combined RNAscope and immunohistochemistry labeling of fresh mouse midbrain tissue
By onHere we describe labeling coronal sections of mouse substantia nigra (SNc) and ventral tegmental area (VTA) for the gene Slc17a6 (VGLUT2) and virally-expressed histone-tagged GFP.
p-S65-Ub sandwich ELISA
By onAssay measures Ubiquitin phosphorylation at Serine-65 in vivo using ELISA. Method previously detailed by Watzlawik et al. in their publication.
Assembly and Use of High Density Silicon Electrophysiology Probes
By onProtocol outlines assembly & use of high-density silicon-based electrophysiological probes in mice. Utilizes devices from Cambridge Neurotech with 3D-printed & machined parts for mounting on mouse head. Recordings done using Intan-based system.
Plasma isolation from whole mouse
By onProtocol describing plasma isolation of adult mice. Used in Palumbos et al., 2025. Adapted from Goldsmith et al., 2022.
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
