Spatial Transcriptomics data (GeoMx) of midbrain dopamine cells in control and PD subjects

This Zenodo deposit contains a publicly available description of the Dataset: Title: "Spatial Transcriptomics data (GeoMx) of midbrain dopamine cells in control and PD subjects". Description: The repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain TH+ cells from Controls (n=10), Incidental Lewy Body Disease (n=10), early Parkinsons Disease (ePD,n=5) and late Parkinsons Disease (lPD,n=5). A total 348 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_edwards_thmask.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-020529) 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本Zenodo存档包含该数据集的公开说明： 标题：《对照与帕金森病（PD）受试者中脑多巴胺能细胞的空间转录组学数据（GeoMx）》 数据集说明：本存档包含通过Nanostring GeoMx（Hu WTA）平台分析得到的空间转录组学数据集，样本取自对照组（n=10）、偶发性路易体病组（n=10）、早期帕金森病组（ePD，n=5）及晚期帕金森病组（lPD，n=5）的中脑酪氨酸羟化酶（tyrosine hydroxylase, TH）阳性细胞，共计分析348个感兴趣区域（Regions of Interest, ROI）。原始计数与标准化计数及元数据以R语言Seurat对象（geomx_edwards_thmask.rds）形式提供。用于低级数据处理的脚本详见：https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md 经病理确认的无症状I-II期路易体病、IV期路易体帕金森病（早期PD）、VI期路易体帕金森病（晚期PD）（Braak等，2003）以及无神经或神经病理疾病的对照组组织样本均取自悉尼脑库。本研究经悉尼大学人类研究伦理委员会批准（审批号：2021/845）。所有帕金森病受试者均对左旋多巴应答良好，且符合英国脑库临床帕金森病诊断标准（Hughes等，1992），无其他神经退行性疾病病史。 未对细胞进行提取操作。研究人员使用轮转式切片机（HistoCore MULTICUT，徕卡生物系统（Leica Biosystems））从死后人类中脑的福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）组织块上切取6μm厚的组织切片，并将其贴附于Series 2粘附式显微镜载玻片（Trajan Scientific Medical，澳大利亚）上，用于后续空间转录组学实验处理。为去除石蜡，载玻片先置于60℃烤箱中孵育1小时，随后浸没于HistoChoice透明剂（Sigma-Aldrich，货号：H2779）中处理2次，每次7分钟；接着依次经梯度乙醇脱水复水：100%乙醇处理2次，每次3分钟，95%乙醇处理3分钟，70%乙醇处理3分钟，最后用蒸馏水浸泡3分钟。 组织切片经酪氨酸羟化酶免疫组化染色后，按照Nanostring GeoMx®数字空间分型仪的制造商操作流程处理感兴趣区域（ROI）。构建的文库在Illumina NovaSeq 6000测序平台上完成测序，所用试剂为NovaSeq SP 100循环试剂盒（XP测序流程，27-8-8-27）。 本研究全部或部分获得帕金森病研究跨学科科学计划（Aligning Science Across Parkinson's, ASAP-020529）通过迈克尔·J·福克斯基金会（Michael J. Fox Foundation for Parkinson's Research, MJFF）提供的资助。为实现开放获取，作者已针对本提交产生的所有作者终稿应用CC BY 4.0公共版权许可。 本数据集通过ASAP CRN云平台（cloud.parkinsonsroadmap.org）向研究人员开放。访问申请流程详见用户手册。 本研究由帕金森病研究跨学科科学合作网络（Aligning Science Across Parkinson's Collaborative Research Network, ASAP CRN）通过迈克尔·J·福克斯基金会（MJFF）资助。 本Zenodo存档由ASAP CRN云平台工作人员代表数据集作者创建，可为CRN云平台数据集提供可引用的参考文献。