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.
-
Output Type
-
Program
-
CRN Team Name
-
Theme
Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients
The dataset includes snRNA-seq data from postmortem brain samples of healthy donors, Parkinson's disease patients, and other neurological disorder patients.
Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x snRNA-seq
Dataset contains snRNA-seq data from postmortem brain samples of healthy donors, Parkinson's patients, and other neurological disorder patients.
Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x multiome (snRNA-seq and snATAC-seq)
Dataset includes snRNA-seq & snATAC-seq data from postmortem brain samples of healthy donors, Parkinson's patients, and other neurological disorders.
Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x snATAC-seq
The dataset includes snATAC-seq data from postmortem brain samples of healthy donors, Parkinson's disease patients, and other neurological disorder patients.
Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – Scale-ATAC + 10x Genomics
Dataset contains ATAC-seq data from midbrain, cingulate cortex, and motor cortex of healthy donors, Parkinson's patients, and other neurological disorder patients.
Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – HyDrop-ATAC v2
The dataset contains snATAC-seq data from postmortem brain samples of healthy donors, Parkinson's disease patients, and other neurological disorder patients.
Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – Scale-ATAC + HyDrop v2
The dataset contains ATAC-seq data from midbrain, cingulate cortex, and motor cortex of healthy donors, Parkinson's patients, and others.
Long read whole genome sequencing data from brain postmortem tissue
Dataset includes 172 whole genome sequencing runs from healthy controls and Parkinson's disease patients, sequenced on Oxford Nanopore platform. Data mapped to T2T-CHM13v2.0 reference genome, available in CRAM format.
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.
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.
Ginkgo bins for hg38 and T2T-CHM13
Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts).
Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
Single-cell long-read sequencing of three brains reveals brain-specific transposable element activity and cell genome dynamics.
