MatLab Code and Source Data for Analyzing Reach-related Single Unit Activity in the Internal Segment of the Globus Pallidus in Parkinsonian Macaque
By onSource data stored in a non-proprietary format, all MATLAB code, along with histology data prepared for the publication of our study on movement-related activity in the internal globus pallidus of parkinsonian macaques (Kase et al. 2025).
FSCV dopamine, spike, and LFP data used for validating chronic electrode implanted in aseptic semi-sealed chamber
By onFSCV dopamine, spike, and LFP data used for validating chronic electrode implanted in aseptic semi-sealed chamber in Choi et al. 2025 JNeurosciMethods.
RNAseq data associated with Moiseyenko et al. 2025
By onBAM files for RNA sequencing of large intestine of wild-type, Thy1-ASO, and Faecalibacterium prausnitzii-treated Thy1-ASO mice from Moiseyenko et al. (2025)
Motor behavior, GI behavior, protein, and volatile fatty acid assay data and analysis code associated with Moiseyenko et al. 2025
By onCode and data used for the statistical analysis of motor behavior and gut physiology tests, and downstream protein assays from Moiseyenko et al. (2025)
Faecalibacterium prausnitzii, depleted in the Parkinson’s disease microbiome, improves motor deficits in α-synuclein overexpressing mice
By onTreatment with an 8-member consortium of bacteria depleted in PD patients, or the single member F. prausnitzii, improves motor and GI function and reduces αSyn aggregates in the brain of a mouse model of PD.
Source data for the article “α-Synuclein aggregation decreases cortico-amygdala connectivity and impairs social behavior in mice”
By onα-Synuclein aggregation in mice reduces cortico-amygdala connectivity, leading to impaired social behavior.
DNA and Expression Following Nucleosome Depletion (DEFND) Sequencing on Cryopreserved Colon Tissue
By onThis protocol details DNA and Expression Following Nucleosome Depletion (DEFND) sequencing optimized for cryopreserved colon tissue.
TheDongLab/EVscope: v1.0.0
By onEVscope is a tool for analyzing extracellular vesicle RNA sequencing data, addressing challenges like low yield and contamination. It includes quality control, alignment, circular RNA detection, expression quantification, and reporting.
Source data for Motor Cortical Neuronal Hyperexcitability Associated with α-Synuclein Aggregation
By onChen et al (2024) study links α-synuclein aggregation to hyperexcitability in motor cortical neurons.
Elevated brain α-synuclein, phosphorylated-tau, and oxidative stress in mice that survived influenza A pneumonitis
By onInfluenza virus infection does not alter acute lung infection course in mice with Lrrk2 mutations. Surviving mice showed elevated neurodegeneration markers post-infection, suggesting a link between influenza and neurodegenerative diseases in humans.
Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
By onOriginal gels with their repeats, associated with pre-print
Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery
By onThis Zenodo deposit is a collection of Microscopy data, KRT, Read me Files associated with the publication "Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery" by Adriaenssens et al.
Tailored workflows for the analysis of transposable elements (Garza et al, 2025)
By onGarza et al. (2025) created customized workflows for transposable element analysis across various data types. Workflows are in Snakemake, Jupyter notebooks, R markdowns, and scripts. Details are in the GitHub README.
Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson’s disease
By onStudy explores transposable elements role in Parkinson's disease neuroinflammation. TE activation in specific brain regions correlates with innate immune responses, indicating potential involvement in chronic neuroinflammation and PD progression.
A molecular atlas of cell-type specific signatures in the parkinsonian striatum
By onProgressive dopamine loss in PD affects striatum cells differently. Transcriptomic analysis in mouse and human models reveals changes in neuronal and glial populations, highlighting resilient and vulnerable cell types for potential new treatments.
Stereotaxic injections of viral vectors and chronic optical fiber implants in mouse brains
By onProtocol details surgical steps for viral injections and optical fiber implantation in mouse striatum to monitor neurotransmitter dynamics during learning and extinction, using genetic sensors and tetanus toxin to suppress acetylcholine release.
Multi-fiber photometry in head-fixed mice performing a dual-cue delay Pavlovian association
By onProtocol describes dual-cue Pavlovian association & multi-fiber photometry in head-fixed mice. Mice trained to link cues with rewards & undergo extinction phase with reduced rewards.
Custom MATLAB scripts related to Bouabid, S. et al. (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations”
By onMATLAB scripts written by Safa Bouabid to analyse ACh release dynamics, DA release, glutamate release onto cholinergic interneurons, and behavioural changes in mouse striatum during learning and extinction of Pavlovian associations.
Custom Phyton scripts related to Bouabid, S. et al (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations””
By onPhyton scripts written by Safa Bouabid and adapted from Han Lab for reading 2D treadmill ball velocity with Raspberry Pi.
Confocal microscopy to assess TelC and iGluSnFR expression in fixed mouse brain slices
By onProtocol outlines tissue processing after glutamate recordings with iGluSnFR sensor & behavior experiments post TelC viral injection in dorsal medial striatum.
