DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.
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DOI：
10.1016/j.csbj.2021.04.021
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发表时间：
2021
影响因子：
6
通讯作者：
Perrimon N
中科院分区：
文献类型：
--
作者：
Hu Y;Tattikota SG;Liu Y;Comjean A;Gao Y;Forman C;Kim G;Rodiger J;Papatheodorou I;Dos Santos G;Mohr SE;Perrimon N
随着单细胞 RNA 测序 (scRNA-seq) 技术的出现，涉及包括果蝇在内的不同物种的多种组织的 scRNA-seq 的研究激增。尽管存在一些数据库供用户查询 scRNA-seq 研究中感兴趣的基因，但使用户能够找到直系同源基因及其跨物种的细胞类型特异性表达模式的搜索工具是有限的。在这里，我们构建了一个新的搜索数据库 DRscDB (https://www.flyrnai.org/tools/single_cell/web/) 来满足这一需求。 DRscDB 是已发布的果蝇 scRNA-seq 数据集以及人类和其他模式生物相关数据集的综合存储库。 DRscDB 基于果蝇 scRNA-seq 研究的手动管理，研究涉及斑马鱼、小鼠和人类等脊椎动物的各种组织类型及其相应的类似组织。值得注意的是，我们的搜索数据库提供了大部分源自文献的标记基因，从而保留了已发表的 scRNA-seq 数据集的原始分析。最后，DRscDB 作为基于网络的用户界面，允许用户从 scRNA-seq 研究中挖掘基因表达数据，并执行与物种内和跨物种的各种 scRNA-seq 研究相关的细胞簇富集分析。
With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in studies involving scRNA-seq of several tissues across diverse species including Drosophila. Although a few databases exist for users to query genes of interest within the scRNA-seq studies, search tools that enable users to find orthologous genes and their cell type-specific expression patterns across species are limited. Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), to address this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets for Drosophila and relevant datasets from human and other model organisms. DRscDB is based on manual curation of Drosophila scRNA-seq studies of various tissue types and their corresponding analogous tissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides most of the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seq datasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expression data from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to various scRNA-seq studies, both within and across species.