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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.
Article
The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability
Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, the authors’ data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Article
Detecting Full-Length EccDNA with FLED and long-reads sequencing
The authors’ method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
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Code
circRNA custom code
Custom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
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Protocol
Confirming circRNA expression by qPCR
This protocol delineates a qPCR method to confirm the expression of circRNAs extracted from brain samples.
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Code
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Power and sample size calculation for bulk tissue and single-cell eQTL analysis based on ANOVA, simple linear regression, or linear mixed-effects model. It can also calculate power/sample size for testing the association of an SNP to a continuous type phenotype.
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Article
Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease
This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA- regulated synaptic specialization in neuropsychiatric diseases.
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Article
α-Synuclein promotes neuronal dysfunction and death by disrupting the binding of ankyrin to β-spectrin
These findings outline a previously undescribed mechanism of α-synuclein neurotoxicity and thus suggest potential new therapeutic approaches in Parkinson’s disease and related disorders.
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Article
Nicotine-mediated rescue of α-synuclein toxicity requires synaptic vesicle glycoprotein 2
Published: Parkinson’s disease likely reflects a complex interaction among genetic and environmental factors. Here, the role of nicotine, SV2 and the alpha-synuclein were examined. The study suggests that SV2 may be needed for the protection nicotine provides from Parkinson’s-related neurotoxicity. View original preprint.
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Code
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
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Article
Targeting cellular senescence with senotherapeutics: senolytics and senomorphics
Review: This article reviews the current state of the development of senolytics and senomorphics for the treatment of age-related diseases and disorders and extension of healthy longevity. In addition, the challenges of documenting senolytic and senomorphic activity in pre-clinical models and the current state of the clinical application of the different senotherapeutics are discussed.
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Dataset
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 circRNAs in this study have been deposited in GEO under accession number GSE218203.
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Protocol
FM1-43 endocytic uptake assay in HIPSC derived neurons
When the cells undergo another stimulation (through KCL or electrical), the FM1-43 dye containing vesicles will be released through exocytosis, thus, resulting in a decrease in the FM1-43 fluorescence intensity.
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Protocol
Nuclei isolation and sorting from frozen human temporal cortex
This protocol is about nuclei isolation and sorting from frozen human temporal cortex.
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Protocol
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.
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