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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.
results for "Team Voet"
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Available ASAP-related hPSC collection from Team Studer
Collection of human pluripotent stem cell lines consisting of isogenic GBA, LRRK2, SNCA series, KI-reporter lines for TOMM20, b-actin, LAMB1, LAMP1, a-synuclein overexpression lines, and other hPSC resources.
Collection of protocols of Team Deleidi used in the publication: “”LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease””
Collection of protocols of Team Deleidi used in the publication: ""LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease""
Collection of protocols for paper: “Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function”
This is a collection of protocols used in a recent preprint by the Deleidi Lab, Team Schapira. You can access pre-print at https://doi.org/10.21203/rs.3.rs-1521848/v1
Evaluating the performance of polygenic risk profiling across diverse ancestry populations in Parkinson’s disease
Objective This study aims to address disparities in risk prediction by evaluating the performance of polygenic risk score (PRS) models using the 90 risk variants across 78 independent loci previously linked to Parkinson’s disease (PD) risk across…
Multi-ancestry genome-wide meta-analysis in Parkinson’s disease
Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, all studies have been performed in just one population at the time. Here we performed the first large-scale…
Human Postmortem-Derived Brain Sequencing Collection (Harmonized Collection)
The Human Postmortem-derived Brain Sequencing Collection is a harmonized repository comprised of sequencing data contributed by ASAP CRN teams.
TULIP – mulTiome demultiplexing Using Long-read SNP Information Pipeline
Snakemake pipeline to demultiplex 10x multiome data utilizing SNP calls from WGS sequencing of pooled patients.
Multiome preprocessing seurat
Workflow to preprocess single nucleus multiome data (gene expression + ATAC) produced with 10X Genomics Cellranger ARC in Seurat.
Methods and applications for single-cell and spatial multi-omics
In this Review, we highlight advances in the developing field of single-cell and spatial multi-omics technologies (multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers.
BIDCell to Seurat
This repository contains an enabler script to convert the BIDcell segmentation output to a Seurat object for the processing of 10X Genomics Xenium spatial transcriptomics data.
Scripts for snRNAseq data analysis
Scripts for analyzing single nuclei sequencing data from healthy and Parkinson's Disease brains include creating a reference database with transposable element annotations and a file for Cell Ranger to produce snRNA count matrices.
Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases
Mouse α-synuclein fibrils have been studied to understand Parkinson's disease and multiple system atrophy. They differ from human fibrils in structure and behavior, impacting research on related diseases and potential treatments.
3D bioprinting of human neural tissues with functional connectivity
Team Scherzer developed a 3D bioprinting platform to assemble tissues with defined human neural cell types in a desired dimension using a commercial bioprinter.
Regional Mouse Brain Analysis (Modified QUINT)
This is series of protocols that has been adapted from published and unpublished protocols broadly referred to as the QUINT workflow: QuPath visualization/segmentation QuickNII Brain Atlas Registration QMask Hemispheric Separation Visualign…
AAV Purification Protocol with Iodixanol gradient
Protocol used in the Kaplitt and Marongiu labs to purify AAVs.