DOI: 10.5281/zenodo.15480996
title: Spatial Transcriptomics data (GeoMx) of midbrain tissue in control and PD subjects

description: This Zenodo deposit contains a publicly available description of the Dataset:

Title: "Spatial Transcriptomics data (GeoMx) of midbrain tissue in control and PD subjects".

Description: he repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain unmasked (whole tissue) Regions of Interest from Controls (n=10), Incidental Lewy Body Disease (n=11), early Parkinsons Disease (ePD, n=5) and late Parkinsons Disease (lPD, n=6). A total 515 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_vila_unmask.rds). The scripts used for low level data processing are described in https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md   Tissue samples from pathologically confirmed asymptomatic stage I-II Lewy body disease, stage IV Lewy body PD (early-PD), stage VI Lewy body PD (late-PD)(Braak, Del Tredici et al. 2003) and controls without the neurological or neuropathological disease were obtained from the Sydney Brain Bank. The study was approved by the University of Sydney Human Research Ethics Committee (2021/845). All cases with PD were levodopa-responsive and fulfilled the UK Brain Bank Clinical Criteria for a diagnosis of clinical PD (Hughes, Ben-Shlomo et al. 1992) with no other neurodegenerative conditions.   Cells were not extracted. Tissue sections were cut from FFPE blocks of post-mortem human midbrains at 6µm on a rotary microtome (HistoCore MULTICUT, Leica Biosystems) and mounted on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for processing for spatial trranscriptomics. To remove the paraffin, slides were incubated in the oven at 60°C for 1hr and then submerged in HistoChoice Clearing Agent (Sigma-Aldrich, H2779) for 2x7mins, followed by rehydration in decreasing ethanol concentrations (100% ethanol for 2x3mins, 95% ethanol for 3mins, 70% ethanol for 3mins) and distilled H2O for 3mins.   Tissue sections were immunohistochemically stained for tyrosine hydroxylase and Regions of Interest (ROIs) processed following Nanostring GeoMx® Digital Spatial Profiler using the manufacturer's instructions. Libraries were sequenced on Illumina Novaseq 6000 platform using NovaSeq SP 100 cycle kit (XP workflow, 27-8-8-27).  This research was funded in whole or in part by Aligning Science Across Parkinson's (ASAP-020505) through the Michael J. Fox Foundation for Parkinson's Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.





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