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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.
Protocol
Analysis of glycosphingolipids from human plasma
The original qualitative method was published in 2004 and measured the oligosaccharides selectively released from glycosphingolipids using a ceramide glycanase enzyme derived from the medicinal leech. This is an updated protocol with the focus on achieving sensitive and reproducible quantitation of glycosphingolipids from human plasma samples
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Western blotting for LRRK2 signalling in macrophages
This protocol describes the immunoblotting for components of the LRRK2 signalling pathway (LRRK2, LRRK2 pS935 and phospho-Rabs) using Invitrogen NuPage SDS-PAGE reagents and the BioRad Turbo Blot transfer system.
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SNP Genotyping and ApoE Genotyping
This protocol details the steps for DNA extraction from a human blood sample, quality control, and SNP and APOE genotyping. The protocol has been adapted from the PRoBaND SNP Genotyping and ApoE Genotyping Protocol
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Sample Collection and Measurement of Serum Neurofilament Light (NfL)
This protocol details the steps for the preparation of serum from human blood samples and the measurement of NfL concentration using the NF-Light Advantage kit on the HD-X Analyzer (Quanterix, Billerica, MA).
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Protein interaction network analysis for Mendelian diseases
This protocol describes the steps to use experimentally validated human data to create a protein-protein interaction network (PPIN) based on disease causative genes. Network analysis (combination of topological functional analyses) will lead to the identification of biological processes relevant for disease and disease endophenotypes.
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In Silico analysis links the NSL complex to Parkinson’s disease and the mitochondria – protein-protein interaction data to functional enrichment analysis
This bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to Parkinson’s disease progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE, and MIST, for curated, literature-derived protein-protein interaction (PPI) data.
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Analysis of glycosphingolipids from human cerebrospinal fluid
The method uses the fluorescent compound anthranilic acid (2-AA) to label oligosaccharides prior to analysis using normal-phase high-performance liquid chromatography. The labeling procedure is rapid, selective, and easy to perform. With the inclusion of a 2AA-labeled chitotriose calibration standard, it is possible to obtain accurate and reproducible molar quantities of individual GSL species.
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Glucosylceramidase Beta (GBA) Genotyping
This protocol has been adapted from the PRoBaND Clinical Consortium (incorporating methods described by Neuman et al., 2009 and Stone et al., 2000) and has been used for all publications for PRoBaND / Tracking Parkinson’s describing clinical data and outcomes with respect to GBA status.
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Luminescent conjugated oligothiophenes (LCO) staining
The protocol describes Luminescent Conjugated Oligothiophenes staining on brain sections.
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Nuclear isolation of post-mortem brain tissue for snRNAseq
This protocol details how to isolate nuclei from frozen brain tissue for single nuclear RNA sequencing using 10x Genomics GEM isolation using the Chromium accessory and Single Cell 3ʹ Reagent Kits.
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Automated immunohistochemistry staining
The protocols describe the steps for automated immunohistochemistry staining using the Ventana Discovery® XT Immunostainer.
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Immunofluorescence staining
The protocol describes immunofluorescence staining on brain sections.
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Formalin fixed Paraffin Embedded (FFPE) Tissue preparation for digital pathology quantification using QuPath
QuPath is an open-source digital pathology analysis software. Here, it is used to quantify various misfolded proteins across anatomical regions. This protocol is appropriate for both human and mouse tissue, and will outline the methods of tissue preparation, digitisation, segmentation, and importing images into QuPath.
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AT8 Tau pathology image analysis
This protocol describes how to analyze AT8 tau pathology in human brain tissue (FFPE sections with IHC).
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