Output 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.
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Output Type
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Program
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CRN Team Name
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Theme
Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
The authors perform metagenomic sequencing of multiple geographically-disparate cohorts and find that stereotypic changes in the functional metabolic potential of the gut microbiome are a consistent feature of PD.
A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice
What should Parkinson's Disease patients eat? This study shows that dietary fiber impacts gut microbes and immune cells in the brain of a mouse model of Parkinson's.
A prebiotic diet modulates microglia response and motor deficits in α-synuclein overexpressing mice
Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic…
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons
Using, highly sensitive ribosome-bound RNA sequencing and imaging to characterize the translatome, the authors uncovered local mRNA translation of dopamine synthesis, release, and reuptake machinery in dendrites, but not axons.
Datasets associated with “Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology”
Dataset associated with the publication "Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology"
Immunohistochemistry (IHC)
Immunohistochemistry for Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Activation Induced Marker (AIM) Staining Protocol
This protocol details about activation induced marker staining.
Fluorescence in situ hybridization (FISH)
Fluorescence in situ hybridization (FISH) in Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain
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.
Intracellular Cytokine (ICS) Staining Protocol
This protocol details about intracellular cytokine (ICS) staining.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Fluorospot SFC
Fluorospot 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"
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
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,…
Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
Dopamine (DA) neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of DA neurons is embedded within complex brain tissues, making it difficult to access the…
Neurite_FISH_Quant–Python code for quantification of FISH puncta in neurites
This repository contains Jupyter Notebooks with Python 3 code for quantification of FISH puncta within neuronal dendrites or axons. However, prior identification of FISH puncta in the images (and optional neurite segmentation) is required. We use…
