ArrayExpress update - from bulk to single-cell expression data.
ArrayExpress update - from bulk to single-cell expression data.
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DOI：
10.1093/nar/gky964
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Brazma A
中科院分区：
文献类型：
--
作者：
Athar A;Füllgrabe A;George N;Iqbal H;Huerta L;Ali A;Snow C;Fonseca NA;Petryszak R;Papatheodorou I;Sarkans U;Brazma A
ArrayExpress(https://www.ebi.ac.uk/arrayexpress)是来自各种技术的功能基因组数据的档案，这些技术分析基因组的功能形态，例如基因表达或启动子占有率。基于测序技术的实验，特别是rna-seq实验的数量在过去几年里一直在增加，在过去的12个月里，提交的测序数据已经超过了微阵列实验。此外，研究单个细胞的实验显著增加，而不是研究被称为单细胞RNA-SEQ的大样本。为了适应这些趋势，我们大幅更改了提交工具Annotare，该工具与原始和处理的数据一起，收集解释这些实验所需的所有元数据。选定的数据集被重新处理并加载到我们的姊妹资源--增值表达式图集(及其组成部分单细胞表达式图集)中，它不仅使用户能够轻松地解释数据，而且还作为数据质量的测试。随着越来越多的研究结合不同的分析模式(多组学实验)，一个新的更通用的档案资源-生物研究数据库已经开发出来，它最终将取代ArrayExpress。数据提交将继续保持不变；所有现有的ArrayExpress数据将被纳入生物研究，现有的登录号和应用程序编程接口将保持不变。
ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments in the last 12 months. Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq. To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments. Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the data easily but also serves as a test for data quality. With an increasing number of studies that combine different assay modalities (multi-omics experiments), a new more general archival resource the BioStudies Database has been developed, which will eventually supersede ArrayExpress. Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained.