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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Single cell eQTL mapping reveals convergent glial–neuronal risk architecture in Parkinson’s disease
Population-scale, disease-context aware meta single-nucleus eQTLs mapping (N = 1,197) in nine cell types from cortex and substantia nigra identifies 125 risk genes and cell types for PD GWAS signals.
Release Notes – ASAP CRN Cloud – Version 4.0.0
ASAP CRN Cloud released version 4.0.0 with expanded datasets including Human Postmortem-derived Brain Sequencing and Mouse datasets. New collections and individual datasets were added, enhancing PMDBS and Mouse RNA sequencing data.
PD5D long read DNA-seq
The dataset includes CCS corrected HiFi lrDNAseq in FASTQ format for 100 PMDBS samples from Parkinson's patients and controls. Part of PD5D atlas, subjects were also profiled with genotyping, single-cell ATACseq, and spatial transcriptomics.
VariantAnalysis: Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
PD5D midbrain single-nucleus RNA-seq hybrid selection
Dataset includes raw FASTQ files from midbrain snRNAseq with hybrid selection for PD5D samples. Subjects also analyzed with DNAseq, genotyping, single-cell ATACseq, and spatial transcriptomics.
Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
Long-read sequencing in PD brain samples identified 74,552 structural variants. Integrating RNA sequencing data revealed SVs near PD-related genes impacting cell type-specific expression, highlighting the importance of SVs in complex diseases.
Nicotine-Mediated Rescue of α-Synuclein Toxicity Requires Synaptic Vesicle Glycoprotein 2 in Drosophila
Background: Parkinson’s disease (PD) is characterized by α-synuclein aggregation and loss of dopamine neurons. Risk of PD arises due to a combination of genetic and environmental factors, which may interact, termed gene-environment (G×E)…
The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability
The paper describes the ability of alpha-synuclein to bind to P-bodies, machinery that regulates the expression of our genes through mRNAs. When alpha-synuclein abnormally accumulates, the physiologic structure and functions of the P-body are lost.
Nuclei Isolation and Sorting from Frozen Human Temporal Cortex V2
Protocol focuses on isolating and sorting nuclei from frozen human temporal cortex.
α-Synuclein Promotes Neuronal Dysfunction and Death by Disrupting the Binding of Ankyrin to β-Spectrin
α-Synuclein plays a key role in the pathogenesis of Parkinson’s disease and related disorders, but critical interacting partners and molecular mechanisms mediating neurotoxicity are incompletely understood. We show that α-synuclein binds…
Confirming circRNA expression by qPCR
This protocol delineates a qPCR method to confirm the expression of circRNAs extracted from brain samples.
FM1-43 endocytic uptake assay in HIPSC derived neurons
FM1-43 is a lipophilic styryl dye, nontoxic to the cells, virtually nonfluorescent in aqueous media. The dye will become fluorescent once it binds to the plasma membrane. In neurons that are actively releasing neurotransmitters, these dyes become…
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
circRNA Custom Code
Custom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
circRNA dataset
New data set on circRNA in laser-captured neuron samples from 190 human brains of healthy controls, prodromal PD, and clinical PD (Dong et al., Nature Communications, in press). The RNA-seq raw FASTQ data and normalized expression matrix of all…
