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 framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
This methods paper outlines silencing transposable elements in hiPSCs using CRISPRi. Describes gRNA design, validation via multiome approach. Enables functional studies on TE transcription in hiPSC models.
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.
TEsingle enables locus-specific transposable element expression analysis at single-cell resolution
TEsingle is a tool for analyzing transposable elements (TE) and gene expression in single-cell data. The tool reveals cell-type specific TE expression in Parkinson's Disease patients' brain tissues.
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.
R Code used in “Sex-Specific Microglial Responses to Glucocerebrosidase Inhibition: Relevance to GBA1-Linked Parkinson’s Disease”
R Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
Indirect Proximity Ligation Assay (PLA) – Brightfield
The authors describe the PLA protocol that is routinely used in the laboratory to detect nitrated alpha-synuclein and nitration of mitochondrial enzymes such as SOD2 and the mitochondrial complex 1 subunit NDUFB8.
Post-fibrillization nitration of alpha-synuclein abolishes its seeding activity and pathology formation in primary neurons and in vivo
Increasing evidence points to post-translational modifications (PTMs) as key regulators of alpha-synuclein (α-Syn) function in health and disease. However, whether these PTMs occur before or after α-Syn pathology formation and their role in…
Single cell/nuclei RNAseq analysis
This protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript “L1retrotransposons drive human neuronal transcriptome complexity and functional diversification ” from fetal forebrain and adult…
Iso-Seq mapping to L1HS/PA2 consensus sequence
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots.
DOPA pheomelanin is increased in nigral neuromelanin of Parkinson’s disease
Neuromelanin in the substantia nigra may be a key factor contributing to dopaminergic neuron vulnerability in Parkinson’s disease. Here, the authors investigated the relative composition and specific roles of pheomelanin and eumelanin in PD.
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in fibroblasts.
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…
Single cell analysis of iPSC-derived midbrain organoids
The following script was used for analysis of gene corrected (GC) versus GBA1 mutant (MUT) midbrain organoids. The purpose was to combine, filter, integrate, and identify clusters and differentially expressed genes sets. This is part of a…
Immunohistochemistry using paraffin embedded tissue
Immunohistochemistry using paraffin embedded tissue
