Image Processing and 3D Reconstruction – Chen et al. 2025 NSMB
By onImage processing and 3D reconstruction applied in Chen et al. 2025 NSMB
Protocols for Goldman et al. 2025
By onAll protocols related to GEM-SCOPe and described in Glodman et al. 2025
Phosphatome-wide siRNA screen in 3T3 cells
By onProtocol details a phosphatome-wide siRNA screen in 3T3 cells to identify phosphatases counteracting LRRK2 for pRab12 and pRab10.
Lysosomal GCase (glucocerebrosidase) activity assay
By onMethod to measure lysosomal GBA1 enzyme activity using 4-MUG substrate at low pH to minimize non-lysosomal GCase interference. GBA1 activity higher in purified lysosomes than whole cell extract, confirmed by CBE inhibitor abolishing 4-MUG hydrolysis.
Preparation of Acute Brain Slices
By onThis protocol describes the steps for preparing acute brain slices.
Electrophysiology and 2-photon imaging of Ca+2-transients
By onProtocol for imaging dendritic calcium transients using 2-photon microscopy with a Ti:Sapphire laser. Fluorescence collected through objective, dichroic mirror, and filters, then detected by a GaAsP PMT. Output digitized for analysis.
Ex Vivo Electrophysiology – Ford Lab
By onThis protocol describes the steps to perform whole-cell electrophysiology recordings in acute brain slices.
Motor Behavioral Assessment
By onProtocol outlines motor behavior tests for Parkinson's disease in mice using open field, rotarod, cylinder, and balance beam tests. Mice were habituated for 30-40 min before tests conducted 3-4 weeks post-injections.
Mouse Whole Gut Transit Time
By onProtocol used in the Gradinaru lab for obtaining whole gut transit time for mice
Mouse Open Field
By onProtocol used in the Gradinaru lab for general locomotion in rodents using open field arenas and Ethovision video tracking
Striatal Punch Collection
By onThis protocol describes how to collect striatal punches from fresh frozen mouse brain tissue for HPLC analysis.
Ex Vivo Mouse Brain Slice Whole-Cell Patch-Clamp Electrophysiology
By onThis protocol outlines steps for performing ex vivo slice whole-cell patch-clamp electrophysiology experiments, including voltage clamp and current clamp recordings as well as optogenetic stimulation in the Ding lab.
Head-fixed Lever-pushing Task in Mice
By onThis protocol describes a head-fixed lever-pushing task used to study motor learning and memory in mice suitable for recording neuronal activity concurrently.
Head-fixed Locomotion Task in Mice
By onThis protocol describes a head-fixed locomotion task used to study motor learning in mice suitable for recording neuronal activity concurrently.
Accelerating Rotarod Task in Mice
By onThis protocol describes an accelerating rotarod task used to study motor learning in mice in the Ding lab.
Optogenetic Silencing of Projection Terminals
By onThis protocol describes the combination of protocols and techniques that are employed to optogenetically silence projections from various areas in the brain.
Steered MD simulations of the inactive-active transition
By onProtocol outlines simulations of PI3KC3-C1 complex transitioning from inactive to active state with RAB1A on a lipid membrane using steered molecular dynamics.
Molecular Dynamics Simulations of Active, Membrane-Engaged Complex
By onThe protocol describes molecular dynamics simulations of PI3KC3-C1 complex with RAB1A on a lipid membrane for studying protein interactions.
