Deep bulk RNAseq of neurological controls and PD brains

This Zenodo deposit contains a publicly available description of the Dataset: Title: "Deep bulk RNAseq of neurological controls and PD brains". Description: Human post-mortem brain tissue from donors with Lewy Body pathology and neurologically healthy controls was sourced from the Cambridge Brain Bank under London–Bloomsbury Research Ethics Committee (REC reference no. 16/LO/0508). Donors with Lewy Body pathology (n=25) had a clinical diagnosis of Parkinson's disease and were compared to an age- and sex-matched group of neurologically healthy control donors (n=18) who had no history of neurological illness. A neuropathologist assessed all cases for Lewy Body pathology Braak staging, co-existing proteinopathies and other pathologies. Fresh frozen tissue was sampled from SN, PUT, AMY, and PFC at the level of Brodmann area 46 (PFC). A 3 mm3 tissue piece was cut from the same tissue block that had been used for snRNA sequencing and disrupted using a Tissuelyser (Qiagen). A steel bead and RLT buffer with -mercaptoethanol was added to the Tissuelyser and shaken at 30 Hz for 2 minutes. Total RNA was isolated from the disrupted tissue using the RNeasy Mini Kit (Qiagen; RRID). The sequencing libraries were then generated using Illumina TruSeq Stranded mRNA library prep kit (with poly-A selection) and sequenced on a NovaSeq6000 or Novaseq X plus (2 x 150 paired end). Basecalling and sample-specific fastq files were done using Illumina's bcl2fastq in default parameters. Reads were uniquely mapped to hg38 reference genome using STAR aligner (version 2.7.8a; REF; RFID, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03). TE and gene quantification was performed using featureCounts (subread package version 1.6.3; REF; RFID -s 2) and gencode annotation version 38, repeatmasker (open-4.0.5, filtered from tRNAs, simple repeats, small RNAs, and low-complexity regions), or retrotector predictions annotation. 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存档包含公开可用的数据集描述： 标题："神经系统健康对照与帕金森病（Parkinson's disease, PD）患者脑组织深度批量RNA测序数据集" 研究样本为来自剑桥脑库（Cambridge Brain Bank）的人类死后脑组织，供体包括路易体病理患者及神经系统健康对照，相关研究已获得伦敦-布鲁姆斯伯里研究伦理委员会批准（伦理编号：16/LO/0508）。其中路易体病理患者（n=25）临床诊断为帕金森病，与年龄、性别匹配且无神经系统疾病史的健康对照供体（n=18）进行对照分析。 所有病例均经神经病理学家评估路易体病理Braak分期、共存蛋白病及其他病理特征。 从黑质（substantia nigra, SN）、壳核（putamen, PUT）、杏仁核（amygdala, AMY）以及布罗德曼46区前额叶皮层（prefrontal cortex, PFC）采集新鲜冻存组织。从该组织块中切取一块3 mm³的样本，该样本此前已用于单细胞核RNA测序（snRNA sequencing），随后使用组织破碎仪（Tissuelyser，Qiagen）进行匀浆：向其中加入钢珠及含β-巯基乙醇的RLT缓冲液，以30 Hz振荡2分钟。 使用RNeasy Mini试剂盒（Qiagen；RRID）从匀浆后的组织中分离总RNA。随后使用Illumina TruSeq Stranded mRNA建库试剂盒（含poly-A富集）构建测序文库，并在NovaSeq6000或NovaSeq X Plus平台完成2×150 bp双端测序。 使用Illumina官方工具bcl2fastq以默认参数完成碱基识别（Basecalling）并生成样本专属fastq文件。使用STAR比对工具（版本2.7.8a；REF；RFID，参数--outFilterMultimapNmax 1、--outFilterMismatchNoverLmax 0.03）将测序reads唯一比对至hg38参考基因组。使用featureCounts（subread软件包版本1.6.3；REF；RFID，参数-s 2）结合GENCODE注释版本38、RepeatMasker（open-4.0.5，已过滤tRNA、简单重复序列、小RNA及低复杂度区域）或Retrotector预测注释，完成转座因子（transposable element, TE）与基因的定量分析。 本数据集通过"跨帕金森病研究协作网络（Aligning Science Across Parkinson's Collaborative Research Network, 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ASAP CRN通过迈克尔·J·福克斯帕金森病研究基金会（Michael J. Fox Foundation for Parkinson's Research, 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。