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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Program
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CRN Team Name
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Theme
Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress
Cryo-ET showed protein aggregates, altered cristae, and reduced ribosome complexes in stressed mitochondria. Mitochondrial Hsp60 undergoes conformational changes to aid in protein folding, shedding light on mitochondrial proteostasis mechanisms.
Cortico-amygdala synaptic structural abnormalities produced by templated aggregation of α-synuclein
PD and DLB involve α-syn inclusions in the amygdala affecting cognition and emotions. Cortico-amygdala synapses with α-syn aggregates show increased volume of synapses, potentially contributing to behavioral impairments.
Single cell eQTL mapping reveals convergent glial–neuronal risk architecture in Parkinson’s disease
We identify 125 functional risk genes for 50 loci—nearly doubling supported genes—and assign genes and cell types to over half of GWAS signals. Unexpectedly, 51% of risk genes are regulated in glia, particularly oligodendrocytes and their…
Protocol to study synapse density or volume— SynDOVE—in brain using confocal microscopy and Imaris three-dimensional surface rendering software
Guide for analyzing for analysis of synaptic loci density and pre- and postsynaptic volumes (SynDOVE). from confocal images of pre- and postsynaptic loci in fixed brain sections with Imaris software.
Copica, an open-source easy-to-use protein copy number mass spectrometry database
Advances in mass spectrometry allow profiling proteome with 10 ng material. Copica database aids in analyzing and comparing protein abundance in cells and tissues, highlighting specific proteins and enabling easy comparison of datasets.
CURTAIN, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS
Curtain is a tool for sharing, visualizing, and analyzing mass spectrometry data, designed for non-experts. It allows easy data sharing via web links and displays differential analysis results in interactive plots.
CURTAIN-PTM, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS (POST TRANSLATIONAL MODIFICATIONS)
Curtain is a tool for sharing, visualizing, and analyzing proteomic and PTM MS data. It allows easy sharing of data via web link, displays results in interactive plots, and enables analysis of protein groups and structure. Free and open-source.
Cactus
Cactus (10.5281/zenodo.7351087) manages session data for curtain and curtainptm backends, handling saving and loading operations efficiently.
CXCL1 supplementation on iPSC-Derived Midbrain Neurons
The protocol studies the impact of different levels of recombinant human CXCL1 on midbrain neurons from iPSCs using conditioned media from ATP13A2WT astrocytes.
Bulk RNA-seq Protocol for Astrocytes
Protocol for RNA extraction from astrocytes for bulk RNA sequencing to analyze gene expression profiles.
ATAC-seq Protocol for Astrocytes
ATAC-seq Protocol for Astrocytes
Bisulfite-seq for Astrocytes
Bisulfite-seq for Astrocytes
SAM ELISA
Protocol for preparing cell lysates and conducting ELISA to quantify proteins is outlined.
CXCL1 ELISA
Protocol for ELISA includes sample prep & assay to quantify antigens in biological samples.
Fluorescently labeled polyamine uptake (via confocal microscopy)
Method visualizes polyamine uptake in cells with fluorescently labeled polyamines & confocal microscopy.
