Single nuclei sequencing of brain regions from healthy and Parkinson's Disease individuals

We performed single nuclei RNA sequencing of postmortem PD and control brain tissue of four different brain regions (substantia nigra, putamen, amygdala, and prefrontal cortex). Briefly, 8500 nuclei were FACS sorted from approximately 2 mm3 of tissue. Single nuclei RNAseq libraries were prepared using 10X genomics platform for single cell 3' sequencing. Sequencing libraries are prepared by fragmentation, end repair and a tailing followed by sample index PCR. To process the data, FASTQ files were processed using Cell Ranger, aligning and quantifying for hg38. Intronic reads were also quantified. 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 Version bump from 2.0 to 2.1 The updated Datasets fix inconsistencies in the ASAP assigned `ASAP_subject_id` and `ASAP_sample_id` for these previously released PMDBS Datasets. These erroneously included the string "PMBDS", now replaced with "PMDBS". This change does not affect the underlying data files, but does update the metadata to be consistent with the naming convention used for all other PMDBS Datasets and the corresponding CDEs.我们对4个不同脑区（黑质、壳核、杏仁核、前额叶皮层）的死后帕金森病（Parkinson's Disease, PD）与对照脑组织开展了单细胞核RNA测序（single nuclei RNA sequencing）。简要流程如下：从约2 mm³的组织样本中，通过荧光激活细胞分选（Fluorescence Activated Cell Sorting, FACS）获得8500个细胞核。单细胞核RNA测序文库采用10X Genomics平台的单细胞3'端测序法制备：测序文库经片段化、末端修复与加尾后，通过样本索引PCR完成构建。数据分析阶段，使用Cell Ranger处理FASTQ文件，针对hg38参考基因组进行比对与定量，同时对内含子读数一并完成定量。 本数据集通过ASAP CRN Cloud（cloud.parkinsonsroadmap.org）向全球研究人员开放。访问申请的详细指引可参阅《用户手册》。 本研究由Aligning Science Across Parkinson's 协作研究网络（ASAP CRN）通过迈克尔·J·福克斯帕金森症研究基金会（Michael J. Fox Foundation for Parkinson's Research, MJFF）资助。 该Zenodo存档由ASAP CRN Cloud工作人员代表数据集作者创建，可为CRN Cloud数据集提供可被引用的参考文献。 本次版本从2.0升级至2.1：本次更新修复了此前发布的PMDBS数据集的ASAP分配字段"ASAP_subject_id"与"ASAP_sample_id"中存在的不一致问题。此前错误包含的字符串“PMBDS”现已替换为“PMDBS”。本次修改未对底层数据文件造成影响，但更新了元数据，使其与所有其他PMDBS数据集及对应公共数据元素（Common Data Elements, CDEs）所采用的命名规范保持一致。