European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
Nucleic Acids Res. 2020 Jan 8;48(D1):D77-D83. doi: 10.1093/nar/gkz947.
Expression Atlas is EMBL-EBI's resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.
表达图谱是 EMBL-EBI 的基因和蛋白质表达资源。它从各种生物系统和环境中获取和编译 RNA 和蛋白质丰度和定位的数据，并为研究界提供对这些数据的开放访问。随着公共档案中单细胞 RNA-Seq 数据集的可用性增加，我们现在已经通过一个新的增值服务扩展了表达图谱，以显示单细胞中的基因表达。单细胞表达图谱于 2018 年推出，目前包含来自 12 个物种的 123 个单细胞 RNA-Seq 研究。用户可以通过种内或种间的基因进行搜索，以揭示该基因表达的实验、组织和细胞类型，以及它在哪些条件下是标记基因。在每个研究中，可以使用预先计算的 t-SNE 图可视化细胞，并根据基因表达将细胞着色为不同的特征或细胞簇。在每个实验中，都有指向可下载文件的链接，例如 RNA 定量矩阵、聚类结果、关于协议的报告以及相关元数据，例如分配的细胞类型。
