WGS data related to “Is Gauchian genotyping of GBA1 variants reliable’
By onGauchian software helps identify GBA1 variants but struggles with rare ones due to database limitations, impacting diagnostic accuracy. Data from this study will aid future research on GBA1 variants.
Source Data and protocols for White, et al 2025- The pyrethroid insecticide deltamethrin disrupts neuropeptide and monoamine signaling pathways in the gastrointestinal tract
By onThe manuscript investigates pyrethroid toxicity in enteroendocrine cells and the gastrointestinal tract. It includes source data, statistical output, qPCR gene expression analysis, RNAseq analysis, Metascape pathway analysis, and key resources.
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 2
By onPart 2 of NGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 1
By onNGS 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.
Global Parkinson’s Genetics Program Data Release 6
By onThis release includes >20,000 additional participants adding to the previous releases from the Complex and Monogenic Networks. The complex disease data (genotypes), including locally-restricted samples, now consists of a total of 44,831 genotyped participants (24,709 PD cases, 17,246 Controls, and 2,876 ‘Other’ phenotypes) The monogenic disease data (whole genome sequences) now consists of a total of 2,324 sequenced participants (1,854 PD cases, 314 Controls, and 156 ‘Other’ phenotypes) 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)."
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
By onSomatic 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.
Alpha-synuclein overexpression can drive microbiome dysbiosis in mice
By onPersons with PD have a distinct gut microbe composition. Studies on gut microbiome changes before and during PD are limited. Overexpression of α-synuclein in mice alters gut bacteria with age, suggesting a link between microbiome and PD pathology.
Ginkgo bins for hg38 and T2T-CHM13
By onVariable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo ().
Dataset: Parkinson’s Families Project: a UK-wide study of early onset and familial Parkinson’s disease
By onParkinson’s Families Project, aims to identify genetic variations linked to familial and early-onset Parkinson's disease. SNP array genotyping, MLPA, and WGS were performed to study pathogenic mutations and their association with clinical factors.
SNP Array Genotyping and Phenotypic Data: “Parkinson’s Families Project: a UK-wide study of early onset and familial Parkinson’s disease”
By onStudy on Parkinson's disease families in the UK collected genotypic data from 698 samples using Illumina NeuroChip SNP Array and phenotypic data from 718 samples. The datasets are publicly accessible via EGA.
