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
DNA and Expression Following Nucleosome Depletion (DEFND) Sequencing on Cryopreserved Colon Tissue
This protocol details DNA and Expression Following Nucleosome Depletion (DEFND) sequencing optimized for cryopreserved colon tissue.
HyDrop-RNA v1.0
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
Single-cell Whole Genome Amplification (scWGA) of human post-mortem brain samples isolated by Laser Capture Microdissection (LCM)
This protocol uses Laser Capture Microdissection (LCM) technology on human post-mortem brain tissue slides in order to do low coverage single-cell whole genome sequencing to detect mega-base somatic Copy Number Variations (CNVs).
HyDrop-ATAC v1.0
Step-by-step protocol for execution of HyDrop-ATAC.
HyDrop Bead Generation & PCR Barcoding v1.0
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
Manual isolation of nuclei from human brain using CellRaft device and single nucleus Whole Genome Amplification
Protocol for manual nuclear isolation from human brain tissue using Cell Raft device for single cell Whole Genome Amplification
Microfluidic Chip Production v1.1 V.2
Protocol for producing microfluidic chips used in HyDrop experiment. Visit for more info
Section 1: Enzymatic DNA Fragmentation (Manually)
This protocol details manual enzymatic DNA Fragmentation prior to Section 2: NGS library preparation for sequencing.
Section 2: NGS library preparation for sequencing
This protocol details NGS library preparation for sequencing and should be performed after Section 1: Enzymatic DNA Fragmentation (Manually).
Section 3: Libraries quality control (QC)
This protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.
Targeted detection of SNCA CNVs in SOX10+ nuclei from oligodendrocytes containing alpha-synuclein inclusions isolated from human post-mortem brain
This protocol describes the detection of low-level genomic mosaics in the human brain using DNA immunofluorescence-fluorescence in situ hybridisation, known as immuno-FISH, to analyze copy number variants in the SNCA gene related to PD & MSA.
Fluorescence-activated nuclei sorting (FANS) for single-cell Whole Genome Sequencing (scWGS)
Protocol for isolating nuclei from human brain samples for low coverage scWGS to detect CNVs. Can be adapted for different body areas, cell cultures, and species.
Nuclei isolation, immunostaining, and Fluorescence-activated nuclei sorting (FANS) for Smart-Seq2
This protocol outlines extracting nuclei from postmortem human brain samples, immunofluorescence, and nuclei sorting for single-nucleus RNA-seq using Smart-Seq2. Applicable to various body areas, cell cultures, and species.
Nova-ST Chip Preparation Protocol
Nova-ST is a high-resolution spatial transcriptomics workflow using nano-patterned Illumina NovaSeq 6000 S4 flow cells. It offers customizable, cost-effective profiling of tissue sections.
Nova-ST Spatial Transcriptomics protocol
Nova-ST is an open-source spatial transcriptomics workflow using high-resolution sequencing, comparable to other methods. It enables flexible and low-cost profiling of tissue sections up to 10mm x 8mm.
