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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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A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex
A data-driven molecular map of the DLPFC reveals distinct spatial domains and cell populations, offering insights into neuropsychiatric disorders. The study provides a roadmap for implementing spatial clustering approaches in the human brain.
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Bioinformatic Prioritisation and Hit Validation
This protocol describes the Bioinformatic Prioritization of PD GWAS candidates for High Content Screening, and Hit Validation by allele-specific expression (ASE) analysis.
Long-read RNA seq analysis using Talon
This is a pipeline that takes fastq data as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts.
Protein aggregation and calcium dysregulation are hallmarks of familial Parkinson’s disease in midbrain dopaminergic neurons
Mutations in SNCA gene cause PD by forming α-synuclein aggregates. Using hiPSCs, we traced pathophysiological events, revealing early oligomeric aggregate formation, calcium signaling impairments, and multiple cellular stresses leading to cell…
The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1
The authors identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity.
SoRA microscopy protocol for imaging oligomers in human brain tissue
This protocol gives a step-by-step guide to imaging oligomers in human brain tissue using a spinning disk confocal microscope.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
ggtranscript simplifies visualizing transcript structure with new geoms like range(), intron(), junction(), and junction_label_repel(). It extends ggplot2's flexibility to create informative plots for publication.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
The authors present ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts from long-read sequences. This tool is an extension of ggplot2.
Splicing accuracy varies across human introns, tissues and age
This in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases
Genetic correlation between neurodegenerative and neuropsychiatric diseases was explored using local rg analysis. Unique relationships were found, suggesting shared genetic mechanisms and potential therapeutic targets in complex diseases.
Live-cell imaging; mitochondrial reactive oxygen species
This protocol presents instructions for assessing mitochondrial souced reactive oxygen species using MitoTracker® Red CM-H2XRos dye.
Genome-wide determinants of mortality and motor progression in Parkinson’s disease
The authors examined the impact of gene variants on mortality and cognitive impairment in PD. Only the non-Gaucher disease causing GBA PD risk variant E326K, of the known PD risk variants, was associated with progression in PD.
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease at 16q11.2 and MAPT H1 loci
Impaired mitophagy is linked to familial PD. New study identifies KAT8 and KANSL1 as regulators of PINK1-dependent mitophagy, suggesting their role in idiopathic Parkinson’s. KANSL1 may be crucial in the disease, offering potential drug targets.
iPS Cell line CRICKi011-A (iFCI016), c.G152A mutation in Exon 3 of SNCA
Mutations in the SNCA gene cause rare autosomal dominant Parkinson’s disease. iPSC lines were created from individuals with SNCA G51D mutations, showing potential for disease modeling and therapy development for synucleinopathies.
iPS Cell line: CRICKi012-A (iFCI017), c.G152A mutation in Exon 3 of SNCA
Mutations in SNCA gene cause rare Parkinson’s disease. iPSC lines from individuals with SNCA G51D mutation were generated successfully, showing normal characteristics. These iPSC lines can aid in studying synucleinopathies for potential therapies.