Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By savannah onDetailed scripts to reproduce all analysis and data visualization for the paper, "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome," including an interactive shiny R app for exploration of metagenomic features of interest in the data sets.
Tissue handling for mice, marmoset, and rhesus macaques injected with AAV
By savannah onThis protocol outlines all procedures for handling of tissue of animal subjects treated with AAV.
Immunohistochemistry of AAV-treated tissues
By savannah onThis protocol outlines procedures to perform immunohistochemistry on tissue that had been treated with AAV.
Images of adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain
By savannah onCAP-Mac, neuron-biased in infant Old-World primates, is shown to have potential for non-invasive systemic gene transfer in the brains of NHPs.
Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain
By savannah onCAP-Mac is shown to have potential for non-invasive systemic gene transfer in the brains of non-human primates.
AAV viral DNA and whole RNA recovery for AAV pool experiments in rhesus macaque
By savannah onThis protocol outlines procedures to extract viral DNA and whole RNA from rhesus macaque tissue that had been treated with AAV in vivo.
Photometry analysis code
By savannah onThis Matlab script extracts GCaMP fiber photometry data and computes the number and amplitude of transients over time.
Mouse brain tissue collection and analysis
By savannah onThis protocol describes the dissection and collection of coronal sections of the striatum and midbrain from a mouse brain.
Mouse behavior – Open Field and T-Maze
By savannah onThis protocol describes two behavioral tasks for mice. The first is the Open Field Test, which is used to asses motor behavior, and the second is the T-Maze, which is used to assess spatial learning.
Live imaging of primary mouse neuron cultures
By savannah onThis protocol describes live imaging of primary neuron cultures. Included are methods for preparing hippocampal or dopamine neuronal cultures from neonatal mouse brain tissue. The imaging technique was used in Jain et al., 2023 to compare vesicular release in neurons between various transgenic knockout mouse lines.
Immunostaining mouse brain tissue or neuronal cultures
By savannah onThis protocol describes immunohistochemical and immunocytochemical methods to analyze protein expression in mouse brain. In the protocol, we describe the fixation of tissue or cultured neurons, the immunostaining procedure, and collecting images for analysis.
Fast Scan Cyclic Voltammetry (FSCV) in mouse brain slices
By savannah onThis protocol describes the method of Fast Scan Cyclic Voltammetry (FSCV) for the application of measuring dopamine transients in mouse brain slices. Within the protocol are sections describing the manufacture of microelectrodes, preparation of acute brain slices, fiber calibration, and measuring stimulated dopamine release.
Single cell transcriptomics from DAT-Cre mouse gut tissue
By savannah onColonic myenteric cells were dissociated, and live tdTomato-positive cells were FACS-collected. Colons were isolated from 2 male and female wild type adult DAT-Cre mice. Wild type C57Bl6/J was used as control for gating. Cells were processed according to 10X Genomics Chromium single cell 3' Reagent guidelines.
Protocols for “Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice”
By savannah onThis is a collection of protocols associated to the manuscript "Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice."
VPS13C^halo∆1235-1748
By savannah onExpress VPS13C truncation mutant in mammalian cells (VPS13C^halo∆1235-1748).
Transfection and protein over-expression
By savannah onThis protocol provides the details for how to transfect and harvest 3X-FLAG-SHIP164Δ901-1099.
siRNA-mediated knockdown of TFE3
By savannah onThis protocol details siRNA-mediated knockdown of TFE3.
RNA isolation and qRT-PCR
By savannah onThis protocol describes the RNA isolation from cultured cells and quantitative RT PCR.
