Targeted long-read RNA-seq
By savannah onTargeted long-read RNAseq of SNCA, GBA1, and GBAP1. The sequencing data is PacBio Sequel IIe targeted Iso-Seq where enrichment was performed using hybridization probes. Three datasets are available: (i) human brain (ii) iPSC-derived astrocytes microglia neurons and (iii) iPSC-derived midbrain dopaminergic neurons.
SoCal Kinesia and Incentivization for Parkinson’s Disease (SKIP): Incentivized Reaching
By savannah onIncentivized Reaching Task from the SKIP Dataset. The Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset facilitates research across human sciences, focusing on human movement and the modulatory impact of incentivization, specifically in the context of Parkinson's disease. This dataset contains data from healthy controls only.
SoCal Kinesia and Incentivization for Parkinson’s Disease (SKIP): Ultra-High Field Functional Connectivity
By savannah onUltra-High Field Functional Connectivity / Network Mapping from the SKIP Dataset. The Socal Kinesia and Incentivization for Parkinson's Disease dataset facilitates research across human sciences, focusing on human movement and the modulatory impact of incentivization, in the context of Parkinson's disease. This dataset contains data from healthy controls.
SoCal Kinesia and Incentivization for Parkinson’s Disease (SKIP): Approach-Avoid
By savannah onApproach-Avoid Task from the SKIP Dataset. The Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset facilitates research across human sciences, focusing on human movement and the modulatory impact of incentivization, specifically in the context of Parkinson's disease (PD). This dataset contains data from healthy controls only.
Microendoscopic calcium imaging in supplementary motor area and primary motor cortex of rhesus macaques at rest and during arm movement
By savannah onMotor cortical regions have undergone evolutionary expansion and specialization from rodents to primates. Studying these regions in non-human primates (NHPs) is relevant to understanding motor control in NHP models of movement disorders. The use of calcium imaging and miniature microscopes allows the study of multiple individual neurons.
RAB32 Ser71Arg in autosomal dominant Parkinson’s disease: linkage, association, and functional analyses
By savannah onRAB GTPases are regulators and substrates of LRRK2, and variants in the LRRK2 gene are important risk factors for Parkinson's disease. Here, the authors explore genetic variability in RAB GTPases within cases of familial Parkinson's disease.
SoCal Kinesia and Incentivization for Parkinson’s Disease (SKIP): Active Escape
By savannah onActive Escape Task (activeescape) from the SKIP Dataset. The Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset facilitates research across human sciences, focusing on human movement and the modulatory impact of incentivization, specifically in the context of Parkinson's disease (PD). This dataset contains data from healthy controls only.
FIJI Syn_Bot Macro
By savannah onAt a neuronal synapse, presynaptic and postsynaptic terminals are ~50nm apart, and thus immunohistochemical staining of a protein from each compartment will give a colocalized signal due to the resolution limits of traditional fluorescence microscopy. This macro counts the number of colocalized synaptic puncta in fluorescence microscopy images.
SNCA transcript diversity in neurons
By savannah onThis repository contains the code used to generate the plots used in the SNCA transcript expression and ASO modulation manuscript.
α-Synuclein overexpression and the microbiome shape the gut and brain metabolome in mice
By savannah onPathological forms of α-synuclein contribute to Parkinson’s disease (PD). Most cases of PD are believed to arise from gene-environment interactions. Microbiome composition is altered in PD, and gut bacteria are causal to symptoms and pathology in animals. Here, the authors explore how the microbiome may impact PD-associated genetic risks.
Data and code for “α-Synuclein Overexpression and the Microbiome Shape the Gut and Brain Metabolome in Mice”
By savannah onMetabolomic data and analysis code associated with the article, "α-Synuclein Overexpression and the Microbiome Shape the Gut and Brain Metabolome in Mice."
Mouse sample collection for metabolomics studies
By savannah onProtocol used in the Mazmanian lab for collecting brain and gut tissues and plasma from mouse for metabolomics.
Quantitative targeted metabolomics for ASO mouse model using Biocrates Q500 platform
By savannah onProtocol for using the Biocrates MxP-Q500 kit (BIOCRATES Life Science AG, Innsbruck, Austria), a commercially-available targeted metabolomics platform, to measure 634 metabolites across 26 biochemical classes from different tissues of the mouse.
SynBot: An open-source image analysis software for automated quantification of synapses
By savannah onQuantifying the number of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. This approach utilizes low-throughput analysis methods that are challenging to learn and results are variable between experimenters. The authors developed SynBot, which automates imaging analysis.
Synapse quantification with Puncta Analyzer
By savannah onProtocol for installing Puncta Analyzer and using it to analyze synapse images.
ilastik install and run for Syn Bot (Windows version)
By savannah onVideo instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Windows operating system.
ilastik install and run for Syn Bot (Mac version)
By savannah onVideo instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Mac operating system.
Installing FIJI and SynBot (Windows version)
By savannah onVideo instructions for installing FIJI and SynBot and a simple SynBot run for Windows operating system.
Activity-dependent remodeling of corticostriatal axonal boutons during motor learning
By savannah onPreprint: The authors assess the activity and structural plasticity of corticostriatal axons during learning in the adult mouse brain.
