Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single-Cell and Spatial Transcriptomic Datasets. Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single-Cell and Spatial Transcriptomic Datasets

To investigate whether large mitochondrial DNA (mtDNA) deletions can be quantified and detected using the high-throughput bioinformatics tool Splice-Break (https://github.com/brookehjelm/Splice-Break2). This dataset contains 8 human middle temporal gyrus (MTG) samples (from 4 patients) that underwent spatial transcriptomic RNA-Sequencing following 10x Genomics visium protocols as well as 2 samples (from spatial transcriptomics patient 144107/144108) that underwent bulk RNA-Sequencing (one with a ribosomal depletion library preparation and one without). Overall design: 10x Visium spatial transcriptomics profiles of middle temporal gyrus tissue taken from 4 patient samples (two tissue sections of each), consisting of 2 controls, 1 Alzheimer's Disease (AD), and 1 Parkinson's Disease (PD). Bulk RNA-Sequencing of one patient with no neurodegenerative diagnosis was included for methods comparison.

本研究旨在探究能否利用高通量生物信息学工具Splice-Break（https://github.com/brookehjelm/Splice-Break2）对大片段线粒体DNA（mitochondrial DNA, mtDNA）缺失进行定量与检测。本数据集包含8例来自4名患者的人类中颞叶（middle temporal gyrus, MTG）样本，所有样本均按照10x Genomics Visium实验流程完成空间转录组RNA测序；此外还包含2例来自空间转录组患者144107/144108的样本，该2例样本完成了批量RNA测序，其中1例采用核糖体耗竭建库策略，另1例未采用该策略。实验整体设计如下：对4例患者的中颞叶组织开展10x Visium空间转录组图谱分析，每例患者包含2张组织切片，其中包括2例对照样本、1例阿尔茨海默病（Alzheimer's Disease, AD）样本以及1例帕金森病（Parkinson's Disease, PD）样本。为进行方法学对比，本数据集同时纳入了1例无神经退行性疾病诊断的患者的批量RNA测序数据。