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: data-analysis
Tutorials for HyDrop data analysis
Probedesign pipeline for the inhouse generation of seqFISH probes
The probe design pipeline works by inputting the transcript id's for probes to be designed. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
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 enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
HyDrop protocol enables single-cell sequencing for RNA and chromatin accessibility. Generated over 7996 single-cell profiles for ATAC-seq and 9508 for RNA-seq in mouse cortex. Protocol validated on low-input samples from Drosophila brain.
Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
The data available in this repository can be used to replicate all the figures in the authors’ manuscript using their data analysis tutorial available at https://github.com/aertslab/hydrop_data_analysis.
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
Detection of mosaic and population-level structural variants with Sniffles2
Sniffles2 is a fast and accurate tool for identifying complex genomic alterations using long -read data.
Microfluidic Chip Production v1.1 V.2
Protocol for producing microfluidic chips used in HyDrop experiment. Visit for more info
Multiple genome alignment in the telomere-to-telomere assembly era
This review provides an overview of the algorithmic template that most multiple genome alignment methods follow.
Sex Distribution of GBA1 Variants Carriers with Dementia with Lewy Bodies and Parkinson’s Disease
Sex Distribution of GBA1 Variants Carriers with Dementia with Lewy Bodies and Parkinson’s Disease
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
Somatic mutations in the brain are well-known, requiring single-cell whole genome amplification before sequencing. PicoPLEX, MDA, and PTA whole genome amplification methods were compared on brain nuclei, showing different properties.
