阿尔茨海默病的单细胞和空间 RNA-seq 数据库 (ssREAD)。
A single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD).
机构信息
Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA.
出版信息
Nat Commun. 2024 Jun 6;15(1):4710. doi: 10.1038/s41467-024-49133-z.
Alzheimer's Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability. The database encompasses 1,053 samples (277 integrated datasets) from 67 AD-related scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells. Additionally, it archives 381 ST datasets from 18 human and mouse brain studies. Each dataset is annotated with details such as species, gender, brain region, disease/control status, age, and AD Braak stages. ssREAD also provides an analysis suite for cell clustering, identification of differentially expressed and spatially variable genes, cell-type-specific marker genes and regulons, and spot deconvolution for integrative analysis. ssREAD is freely available at https://bmblx.bmi.osumc.edu/ssread/ .
阿尔茨海默病（AD）的病理学研究越来越多地通过单细胞和单核 RNA 测序（scRNA-seq 和 snRNA-seq）和空间转录组学（ST）进行探索。然而，数据的激增需要一个全面、用户友好的资源库。为了解决这个问题，我们引入了一个用于阿尔茨海默病的单细胞和空间 RNA-seq 数据库（ssREAD）。它提供了更广泛的 AD 相关数据集、优化的分析管道和更好的可用性。该数据库包含来自 67 项 AD 相关 scRNA-seq 和 snRNA-seq 研究的 1053 个样本（277 个集成数据集），总计 7332202 个细胞。此外，它还存档了来自 18 个人类和小鼠大脑研究的 381 个 ST 数据集。每个数据集都用详细信息进行注释，如物种、性别、大脑区域、疾病/对照状态、年龄和 AD Braak 阶段。ssREAD 还提供了一个用于细胞聚类、差异表达和空间可变基因、细胞类型特异性标记基因和调控网络以及集成分析的斑点去卷积的分析套件。ssREAD 可在 https://bmblx.bmi.osumc.edu/ssread/ 免费获取。
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