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Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
Dataset
Fecal metagenomic sequencing data for PD patients and controls from the BioCollective
Fecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.
Code
Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
Detailed 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.
Article
Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
Preprint: Here, the fecal metagenomes of those living with PD compared to others in the household were profiled from 4 geographically-distinct sites across 3 continents. The question was whether there were any specific PD-associated signatures in gut microbiome that are either enriched or depleted in PD.
Dataset
Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center
Fecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.
Article
Dopamine transporter and synaptic vesicle sorting defects initiate auxilin-linked Parkinson’s disease
Published: Auxilin helps in recycling of synaptic vesicles to facilitate neurotransmission and loss of auxilin is associated with PD. The authors show auxilin knockout mice exhibit typical PD pathology, dopamine transport is disrupted due to slower dopamine reuptake kinetics, and that macroautophagy and defective synaptic vesicle sorting contributes to dopamine dyshomeostasis. View original preprint.
Dataset
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures – Gene Validation FCS
FCS files corresponding to the gene validation experiment described in “Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures.”
Teams
Dataset
Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
The 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).
Teams
Dataset
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures – Cell Surface FCS
FCS files corresponding to the cell surface experiment described in “Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures.”
Teams
Article
Similarities and differences between nigral and enteric dopaminergic neurons unravel distinctive involvement in Parkinson’s disease
Review: In this comparative review, authors compare the Dopamine neurons in the enteric nervous system, substantia nigra pars compacta, and ventral tegemental area, to assess whether, independent of their location or function, it is sufficient for neurons to be dopaminergic to be selectively vulnerable during the progression of PD.
Teams
Dataset
ENS quantification
Labelled 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.
Teams
Dataset
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons
This 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).
Teams
Dataset
A single-cell atlas of cell types, states, and other transcriptional patterns from nine regions of the adult mouse brain
We 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).
Teams
Dataset
Peripheral neuronal activation of the intestinal tract shapes the microbiome and alters gut physiology-RNAseq
This RNA data set corresponds to the preprint: Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice (Yoo et al., 2021).
Teams
Code
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons – DropSeqPipeline8
This 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.
Teams