Expression Atlas update: from tissues to single cells
Expression Atlas update: from tissues to single cells
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DOI：
10.1093/nar/gkz947
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Brazma, Alvis
中科院分区：
文献类型：
--
作者：
Papatheodorou, Irene;Moreno, Pablo;Brazma, Alvis
表达地图集是Embl-Ebi的基因和蛋白质表达的资源。它来源和编译了有关RNA和蛋白质在各种生物系统和环境中的丰度和定位数据的数据，并为研究界提供了对该数据的开放访问。随着公共存档中单细胞RNA-seq数据集的可用性增加，我们现在已经扩展了具有新的添加值服务的表达地图集，以在单个细胞中显示基因表达。单细胞表达地图集于2018年推出，目前包括来自12种的123个单细胞RNA-seq研究。可以通过物种内部或各种基因搜索该网站，以揭示该基因表达的实验，组织和细胞类型，或者在哪种条件下它是标记基因。在每项研究中，都可以使用预缩的T-SNE图可视化细胞，并且可以通过不同特征或基于基因表达的细胞簇进行色彩。在每个实验中，都有与可下载文件的链接，例如RNA量化矩阵，聚类结果，协议和相关元数据的报告，例如分配的单元格类型。
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.