PD5D_MTG_Visium10x_ST

This Zenodo deposit contains a publicly available description of the Dataset: "PD5D_MTG_Visium10x_ST". Dataset Description: Visium 10x spatial transcriptomic raw data in FASTQ format of the middle temporal gyrus of 96 human subjects. Individuals with incidental Lewy body disease, clinical PD, and healthy control were included. In addition to subject level metadata, Visium spatial metadata such as H&E images and spot coordinates are included. These data are one component of the PD5D cohort, which intends to build a multi-dimensional and multi-omic atlas of PD pathology. For the same subjects, other omics assays have been collected including genotyping, snRNA-seq, and scATAC-seq across two brain tissues: middle temporal gyrus and substantia nigra. Authors: • Scherzer, Clemens; ORCID:0000-0002-0567-9193 • Dong, Xianjun; ORCID:0000-0002-8052-9320 • Levin, Joshua; ORCID:0000-0002-0170-3598 • Serrano, Geidy; ORCID:0000-0002-9527-2011 • Beach, Thomas; ORCID:0000-0003-3296-6128 • Liao, Zhixiang; ORCID:0000-0001-7014-5465 • Tuncali, Idil; ORCID:0000-0001-5549-3082 • Parker, Jacob; ORCID:0000-0001-9425-6418 • Yuan, Jie; ORCID:0000-0002-5626-2881 • Haywood, Nathan; ORCID:0000-0003-2213-5080 • Simmons, Sean; ORCID:0000-0002-1537-4000 • Adiconis, Xian; ORCID:0000-0002-4052-2503 • Weykopf, Beatrice; ORCID:0000-0001-5541-839X ASAP Team: Scherzer Dataset Name: scherzer-pmdbs-spatial-visium-mtg, v1.0 Principal Investigator: Xianjun Dong, [email protected] Dataset Submitter: Dr. Jie Yuan, [email protected] Publication DOI: NA Grant IDs: ['ASAP-000301'] ASAP Lab: Scherzer, Dong, and Levin ASAP Project: Parkinson5D: deconstructing proximal disease mechanisms across cells, space, and progression Project Description: Here we will develop a molecular atlas of Parkinson's disease (PD) useful for mapping GWAS/familial genetics to proximal mechanisms in five dimensions: brain cells (1D), brain space (3D), and disease stage (1D). We will reveal how genetic variants modulate transcription in specific cells in specific topographic locations of midbrain and cortex during the progression of neuropathology from healthy brains to prodromal to symptomatic disease. This research will for the first time integrate whole genome sequencing, single-nucleus transcriptomics, and high-resolution spatial transcriptomics of 100 human brains with cell-specific mechanistic analyses in model systems. Submission Date: 2025-10-30 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