Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden.
Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, Mölndal, Sweden.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz046.
Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to access for biological researchers due to the need for data processing using complex computational pipelines. We have implemented an online database, PanglaoDB, accessible through a user-friendly interface that can be used to explore published mouse and human single cell RNA sequencing studies. PanglaoDB contains pre-processed and pre-computed analyses from more than 1054 single-cell experiments covering most major single cell platforms and protocols, based on more than 4 million cells from a wide range of tissues and organs. The online interface allows users to query and explore cell types, genetic pathways and regulatory networks. In addition, we have established a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types.
单细胞 RNA 测序是一种越来越常用的方法，用于测量单细胞水平的基因表达，并构建组织的细胞类型图谱。已经发表了数百个单细胞测序数据集。然而，由于需要使用复杂的计算管道进行数据处理，因此这些研究经常以原始数据的形式存储，这对于生物研究人员来说难以访问。我们已经实现了一个在线数据库 PanglaoDB，可通过用户友好的界面访问，可用于探索已发表的小鼠和人类单细胞 RNA 测序研究。PanglaoDB 包含来自 1054 多个单细胞实验的预处理和预先计算的分析，这些实验基于来自广泛的组织和器官的超过 400 万个细胞，涵盖了大多数主要的单细胞平台和方案。在线界面允许用户查询和探索细胞类型、遗传途径和调控网络。此外，我们还建立了一个社区管理的细胞类型标记物汇编，包含超过 6000 个基因-细胞类型关联，作为细胞类型自动注释的资源。
