Golgi immunopurification (Golgi-IP) for subcellular metabolite profiling
By savannah onThis protocol provides details for preparing Golgi-IP metabolomics samples.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures – Gene Validation FCS
By savannah onFCS files corresponding to the gene validation experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures."
Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
By savannah onThe elaborate cytoarchitecture of DA neurons is embedded within complex brain tissues, making it difficult to access the DA neuronal proteome using conventional methods. This mass spectrometry proteomics dataset is a part of "Subcellular proteomics of dopamine neurons in the mouse brain" (Hobson et al., 2022).
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures – Cell Surface FCS
By savannah onFCS files corresponding to the cell surface experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures."
Primary data associated with the manuscript “Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content” (doi.org/10.1101/2022.11.22.517583)
By savannah onRaw data files used for the manuscript "Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content" (doi.org/10.1101/2022.11.22.517583).
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures – Fluorospot SFC
By savannah onFluorospot SFC (combined IFNg, IL-5, and IL-10) data and corresponding HC-PD group IDs described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures."
ENS quantification
By savannah onLabelled enteric neurons in living mice with recombinant adeno-associated viruses (rAAVs) expressing fluorescent proteins, and used tissue clearing techniques to enhance visualization of intact GI tissue.
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons
By savannah onThis dataset is a part of "Subcellular and regional localization of mRNA translation in midbrain dopamine neurons" (Hobson et al., 2022) where the authors investigated mRNA localization in midbrain dopaminergic (mDA) neurons, cells with enormous axonal and dendritic projections, both of which can release dopamine (DA).
A single-cell atlas of cell types, states, and other transcriptional patterns from nine regions of the adult mouse brain
By savannah onWe report 690K single-cell transcriptomes from nine different brain regions from adult mice (Frontal and Posterior Cortex, Hippocampus, Thalamus, Cerebellum, Striatum, Globus Pallidus externus/Nucleus Basalis, Entopeduncular / Subthalamic Nuclei, & Substantia Nigra / Ventral Tegmental Area).
Datasets associated with “Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology”
By savannah onThis RNA data set corresponds to the preprint: Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice (Yoo et al., 2021).
katiekellyucl/W-PPI-NA-NSL-complex: v1.0.0. W-PPI-NA/NSL_complex
By savannah onSoftware for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis).
Image analysis for Jensen et al., 2022
By savannah onPython script for image analysis in Jensen et al., 2022.
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons – DropSeqPipeline8
By savannah onThis is a data processing pipeline for analyzing microwell- or DropSeq-like scRNA-seq data. It can also be used for analyzing pooled plate-based scRNA-seq.
Mouse reaching task
By savannah onThis repository contains all the materials to build the mouse-reaching task and analyze the data acquired with this task.
Python script for Golgi cytoscape analysis
By savannah onCustom Python script used for the cytoscape network analysis reported in doi.org/10.1101/2022.11.22.517583 (Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content).
Orchestration of selective autophagy by cargo receptors
By savannah onReview: Selective autophagy represents a major pathway for the degradation of cargo material. The authors review recent insights into the mechanisms of action of cargo receptors in selective autophagy by focusing on the roles of sequestosome-like cargo receptors in the degradation of misfolded, ubiquitinated proteins and damaged mitochondria.
Rapid iPSC inclusionopathy models shed light on formation, consequence, and molecular subtype of α-synuclein inclusions
By savannah onPublished: Intracellular inclusions accompanying neurodegeneration are histopathologically and ultrastructurally heterogeneous but the significance of this heterogeneity is unclear. iPSC models do not form inclusions in a reasonable timeframe and suffer from limited tractability. The authors developed an iPSC toolbox utilizing piggyBac-based or targeted transgenes to rapidly induce CNS cells with concomitant expression of aggregation-prone proteins. View original preprint.
Serine-129 phosphorylation of α-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function
By savannah onPublished: Phosphorylation of α-synuclein at the Serine-129 site (α-syn Ser129P) is an established pathologic hallmark of synucleinopathies and also a therapeutic target. Exploring AlphaFold2-driven modeling and membrane-binding simulations, the authors offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug development. View original preprint. View original preprint.
Novel green fluorescent polyamines to analyze ATP13A2 and ATP13A3 activity in the mammalian polyamine transport system
By savannah onPreprint: Cells acquire the polyamines putrescine (PUT), spermidine (SPD), and spermine (SPM) via the complementary action of polyamine uptake and synthesis pathways. The endosomal P5B-type ATPases ATP13A2 and ATP13A3 emerge as major determinants of mammalian polyamine uptake. Our biochemical evidence shows that fluorescently labeled polyamines are genuine substrates of ATP13A2.
Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content
By savannah onPublished: Traditional methods are too slow to preserve the labile Golgi metabolome and transient protein interactions. Here, the authors develop a method for the rapid capture of intact Golgi from human cells via Golgi immunoprecipitation (Golgi-IP). Using high-resolution mass spectrometry, the approach allows the unbiased characterization of the Golgi proteome, metabolome, and lipidome.
