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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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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.
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…
Towards a phenome-wide view of Parkinson’s disease
Many studies have examined the relation between PD and environmental variables serially — one candidate association at a time. In the real world however, both environmental exposures and patients are much more complex, including correlated…
Transferrin uptake assay to measure Clathrin-mediated endocytosis in HIPCS derived neurons
This protocol is used to measure Transferrin uptake as a way to investigate Clathrin-mediated endocytosis in HIPCS derived neurons, or other cell types.
Sample Collection and Processing for RNA Analysis
This protocol delineates the steps taken to collect frozen postmortem human brain samples and process them for RNA extraction and analysis.
Detecting Full-Length EccDNA with FLED and long-reads sequencing
Reconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given the similarity of eccDNAs and their corresponding linear DNAs. Previous sequencing methods were unable to…
powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
Genome-wide association studies (GWAS) have revealed thousands of genetic loci for common diseases. One of the main challenges in the post-GWAS era is to understand the causality of the genetic variants. Expression quantitative trait locus (eQTL)…
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Easy-to-use web application for calculating sample size and power of bulk tissue and single-cell eQTL analysis