Immunofluorescent labeling of preformed fibril protein protocol
By Emma Sherrell onThis protocol details the use of an AlexaFluor 488 protein labeling kit to fluorescently label alpha synuclein preformed fibril protein for future application.
LRRK2-G2019S synergizes with aging and low-grade inflammation to promote gut and peripheral immune cell activation that precede nigrostriatal degeneration
By savannah onDataset collection related to preprint, "LRRK2-G2019S Synergizes with Aging and Low-Grade Inflammation to Promote Gut and Peripheral Immune Cell Activation that Precede Nigrostriatal Degeneration."
Western blot: Alpha-synuclein
By savannah onThis protocol describes how to detect alpha-synuclein protein in mouse dorsal medulla oblongata tissue by western blot.
Hutu80 and NCI h716 treatment with SCFAs and α synuclein Western blotting
By savannah onThis protocol describes the treatment of human enteroendocrine cell models Hutu80 and NCI h716 parental cells with SCFAs and GCase inhibitor (CBE) in order to detect the impact of SCFAs and GCAse inhibition on alpha synuclein protein expression by immunoblotting.
Human embryonic kidney cells (HEK-293)
By Emma Sherrell onThis protocol is a basic description of maintenance and culturing of human embryonic kidney cells (HEK-293).
Immunofluorescence labeling and imaging of cholinergic interneurons in post-mortem human brain tissues
By savannah onThis protocol details immunofluorescence labeling and imaging of cholinergic interneurons along with striatal astrocytes in formalin-fixed paraffin-embedded (FFPE) post-mortem human brain tissues.
Lysosomal activity DQ-Red BSA assay
By Emma Sherrell onThis protocol details the lysosomal activity DQ-Red BSA Assay. This is for treatment to live cells followed by fixation for imaging. Red signal is detected only when fluorogenic substrate is hydrolyzed by lysosomal proteases.
Imaging of cholinergic interneurons in post-mortem rodent tissue to identify striatal satellite astrocytes
By savannah onThis protocol explains steps for confocal imaging and analysis to measure inter-soma distance between interneurons/pMSNs & nearest astrocyte.
In vitro αS PFF treatment
By Emma Sherrell onThis protocol details the preparation of alpha synuclein preformed fibrils for in vitro treatment to cells for the analysis of protein uptake and processing or clearance.
Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data
By Emma Sherrell onThe authors systematically investigated experimental and computational design choices for their effects on allelic imbalance analysis in droplet-based snRNA-seq data from human samples. They also show many factors including read length and sequencing technology.
manuelatan/PD-survival-GWAS: Release 2.0
By Emma Sherrell onCode for PD progression survival GWAS to mortality, and Hoehn and Yahr stage 3 or greater (H&Y3+) to understand the determinants of mortality and motor progression in Parkinson’s disease.
Fecal sample collection
By Emma Sherrell onFecal sample collection from mice to use for gut microbiome sequencing analysis.
Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices while optogenetically activating astrocytes
By savannah onThis protocol assesses whether optogenetically activating astrocytes affects the dopamine concentration released following electrical stimulation.
Voltage sensor imaging in a population of dopaminergic axons in the mouse striatum
By savannah onThis protocol details steps for voltage sensor imaging in striatal dopaminergic axons on mouse brain slices using the ASAP5f sensor from the Michael Lin Lab.
Operant behavior
By Emma Sherrell onThis protocol is for training mice operant conditioning to assess cognitive performance using the resources described in Matikainen-Ankney BA et al. 2021.
ATG3 research outputs_discontinued
By savannah on(https://docs.google.com/spreadsheets/d/1Wdx_852CaqRRkGTbrZTKnYch2eiRN74A/edit?usp=sharing&ouid=109625585762898855018&rtpof=true&sd=true) lists all ATG3 discontinued research outputs generated for https://www.biorxiv.org/content/10.1101/2023.07.17.549391v2 but not published in https://www.science.org/doi/10.1126/sciadv.adj8027 as they were deemed to be "not effective." These cell lines were replaced by another set published on the Hub.
Development of a simplified smell test to identify patients with typical Parkinson’s as informed by multiple cohorts, machine learning and external validation
By Emma Sherrell onReduced olfaction is a common feature of typical Parkinson's disease (PD) and dementia with Lewy bodies (DLB). The authors created a simplified smell test based on seven specific odorants that can distinguish PD/DLB patients from healthy controls.
