Genotype of subjects contributing PMDBS samples. This dataset details the genotype for subjects contributing samples to our snRNAseq PMDBS datasets (e.g. scherzer-sn-rnaseq-mtg and scherzer-sn-rnaseq-mtg-hybsel) as a tar.gz archive of PLINK outputs (.bed, .bim, .fam, .log, and .nosex files).Methods Summary: All subjects were genotyped by Multi-Ethnic Genotyping Array (MEGA) using the Infinium Multi-Ethnic Global-8 v1 kit (Illumina, #WG-316-1001) following manufacturer’s instructions and using the DNA extracted from brain tissue. Additional information about this chip, pls see: https://support.illumina.com/downloads/infinium-multi-ethnic-global-8-v1-support-files.html. PLINK (v1.9beta) were applied to perform rigorous subject and SNP quality control (QC) for each dataset in the following order (Extended Data Fig.1): (1) remove variants with GenCall score (GC) < 0.15;  (2) remove subjects with call rate < 95%; (3) remove subjects with gender misidentification; (4) remove SNPs with genotype call rate < 95%; (6) remove SNPs with Hardy-Weinberg Equilibrium testing P value < 1e-6; (6) remove SNPs with informative missingness test (Test-mishap) P value < 1e-9; (7) remove SNPs with minor allele frequency (MAF) < 0.01; (8) remove subjects with outlying heterozygosity rate based on heterozygosity F score (beyond 4-fold sd from the mean F score); (9) IBS/IBD filtering: pairwise identity-by-state probabilities were computed for removing both individuals in each pair with IBD>0.9 and one subject of each pair with IBD > 0.1875; (10) Subjects were integrated with 1000 Genomes phase3 individuals and tested for population substructure by performing principal components analysis (PCA) using PLINK. Based on first and second principal components, significant genotypic outliers (non-European individuals) were excluded.

We're excited to announce the v2.0.0 release of the Postmortem-derived Brain Sequencing Single Cell (sc)RNAseq Collection to the ASAP CRN Cloud as part of the v2.0.0 Release (10.5281/zenodo.14270014).  There are additional datasets in the collection since previous releases, and a newly updated Cohort datasets of scRNAseq samples integrated across the individual Team contriubuted datasets. Stay Tuned!

This dataset was obtained using CSF samples of the Harvard Biomarker Study (HBS). HBS is a case-control study including 3,000 patients with variousneurodegenerative diseases as well as healthy controls (HC).Human CSF was analyzed with BASF Metabolome Solutions GmbH. Data were used in the preprint: Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s diseasedoi: https://doi.org/10.1101/2024.05.15.594309

This dataset was obtained using CSF samples of the Harvard Biomarker Study (HBS). HBS is a case-control study including 3,000 patients with variousneurodegenerative diseases as well as healthy controls (HC).Human CSF was analyzed with BASF Metabolome Solutions GmbH. Data were used in the preprint: Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s diseasedoi: https://doi.org/10.1101/2024.05.15.594309

Correct DOI: 10.5281/zenodo.16751625.

This Zenodo deposit contains a publicly available description of the Dataset:Title: "PD5D_MTG_snRNAseq_hybsel".Description: This dataset contains the raw data in FASTQ format for single-nucleus RNA sequencing (snRNAseq) enriched with Agilent SureSelect for reads from a list of targeted transcripts for human middle temporal gyrus (MTG) samples from Parkinson's patients and healthy controls. This data comes from the same 10X libraries as PD5D_MTG_snRNAseq, except with the additional enrichment step before sequencing. It's part of the PD5D cohort, where the same subjects were also profiled with other omics assays incl. genotyping, single-cell ATACseq, and spatial transcriptomics.This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

This Zenodo deposit contains a publicly available description of the Dataset:Title: "PD5D_MTG_snRNAseq_hybsel".Description: This dataset contains the raw data in FASTQ format for single-nucleus RNA sequencing (snRNAseq) enriched with Agilent SureSelect for reads from a list of targeted transcripts for human middle temporal gyrus (MTG) samples from Parkinson's patients and healthy controls. This data comes from the same 10X libraries as PD5D_MTG_snRNAseq, except with the additional enrichment step before sequencing. It's part of the PD5D cohort, where the same subjects were also profiled with other omics assays incl. genotyping, single-cell ATACseq, and spatial transcriptomics.This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

This Zenodo deposit contains a publicly available description of the Dataset:Title: "PD5D_MTG_snRNAseq_hybsel".Description: This dataset contains the raw data in FASTQ format for single-nucleus RNA sequencing (snRNAseq) enriched with Agilent SureSelect for reads from a list of targeted transcripts for human middle temporal gyrus (MTG) samples from Parkinson's patients and healthy controls. This data comes from the same 10X libraries as PD5D_MTG_snRNAseq, except with the additional enrichment step before sequencing. It's part of the PD5D cohort, where the same subjects were also profiled with other omics assays incl. genotyping, single-cell ATACseq, and spatial transcriptomics.This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

We're excited to announce the availability of the Version 1.0.0 data release on the CRN Cloud! In this release, we have expanded data collections with contributions from Team Scherzer. Furthermore, we've updated the Postmortem-derived Brain Sequencing Collection by integrating this team’s data into the harmonized subset. This curated subset now contains data from a total of 156 subjects from 4 CRN Teams and is organized across common data elements.The current data collections represent the minimum viable product and are being expanded as additional data is uploaded into the CRN Cloud. When complete, the collection will provide data generated from 1,800+ samples using proteomics, transcriptomics, and sequencing (single-nucleus RNAseq, single-cell RNAseq, bulk RNA-seq, ATAC-seq, long read WGS, and single-nucleus multiome sequencing (paired snRNAseq, snATACseq)) techniques.

Correct DOI: 10.5281/zenodo.16751625.