Release Notes – ASAP CRN Cloud – Version 4.0.0
By onASAP CRN Cloud released version 4.0.0 with expanded datasets including Human Postmortem-derived Brain Sequencing and Mouse datasets. New collections and individual datasets were added, enhancing PMDBS and Mouse RNA sequencing data.
PD5D long read DNA-seq
By onThe dataset includes CCS corrected HiFi lrDNAseq in FASTQ format for 100 PMDBS samples from Parkinson's patients and controls. Part of PD5D atlas, subjects were also profiled with genotyping, single-cell ATACseq, and spatial transcriptomics.
DNA methylome profiling (Bisulfite Sequencing) of human iPSC-derived midbrain astrocytes in ATP13A2 c.1306deficiency models
By onDataset offers DNA methylation profiles of human midbrain astrocytes comparing ATP13A2 c.1306 mutants with Wild Type controls using WGBS.
Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x snATAC-seq
By onThe 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 – HyDrop-ATAC v2
By onThe 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 + 10x Genomics
By onDataset 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 – Scale-ATAC + HyDrop v2
By onThe 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
By onDataset 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.
Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center
By onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.
Global Parkinson’s Genetics Program Data Release 5
By onThis release includes 7,462 additional new complex disease participants and 487 new monogenic disease participants, adding to the previous releases from the Complex and Monogenic Networks. The complex disease data (genotypes) now consists of a total of 24,935 genotyped participants (12,728 PD cases, 10,533 Controls, and 1,674 ‘Other’ phenotypes). The monogenic disease data (whole genome sequences) now consists of a total of 722 sequenced participants. For any publications using data from this release, please reference the DOI number and the following statement: "Data (DOI 10.5281/zenodo.7904832, release 5) used in the preparation of this article were obtained from the Global Parkinson’s Genetics Program (GP2)."
Highly efficient generation of isogenic pluripotent stem cell models using prime editing – Datasets
By onThis collection contains the following datasets related to the paper Highly efficient generation of isogenic pluripotent stem cell models using prime editing 1. AAVS1 knock-in genotyping 2. aCGH karyotyping 3. Tabular datasets for associated graphical figures
Time to LiD GWAS dataset
By onCode to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses
Genome-wide determinants of mortality and clinical progression in Parkinson’s disease – Summary statistics
By onSummary statistics from "Genome-wide determinants of mortality and clinical progression in Parkinson’s disease."
Fecal metagenomic sequencing data for PD patients and controls from the BioCollective
By onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the BioCollective cohort.
Bulk NGS/allele quantification – Highly efficient generation of isogenic pluripotent stem cell models using prime editing
By onThis file contains sequencing results for amplicons covering specific regions of interest related to prime editing of hPSCs
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 1
By onNGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 2
By onPart 2 of NGS data associated with Uoselis et al., 2023.
Next-generation sequencing of AAV.CAP-Mac enrichment from Chuapoco et al. (2023)
By onDataset of next-generation sequencing of enrichment of AAV.CAP-Mac in various tissues from the publication: Chuapoco, M.R., Flytzanis, N.C., Goeden, N. et al. Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. Nat. Nanotechnol. (2023). https://doi.org/10.1038/s41565-023-01419-x
Saliva metagenomic data related to “Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics”
By onIn this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, by significantly producing higher DNA fragment sizes, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
Characterizing dysbiosis of the Parkinson’s disease gut microbiome using shotgun metagenomics
By onParkinson's disease is a progressive neurodegenerative condition with altered gut microbiome composition. A study analyzed fecal samples from 490 PD patients and 234 healthy individuals to understand dysbiosis at a detailed level.
