SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics Pub Date : 2024-01-11 DOI:10.1093/gpbjnl/qzae005

Zekai Liu, Zhen Yuan, Yunlei Guo, Ruilin Wang, Yusheng Guan, Zhanglian Wang, Yunan Chen, Tianlu Wang, Meining Jiang, Shuhui Bian

{"title":"SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine","authors":"Zekai Liu, Zhen Yuan, Yunlei Guo, Ruilin Wang, Yusheng Guan, Zhanglian Wang, Yunan Chen, Tianlu Wang, Meining Jiang, Shuhui Bian","doi":"10.1093/gpbjnl/qzae005","DOIUrl":null,"url":null,"abstract":"Abstract Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here we introduce the single-cell multi-omics atlas of reproduction (SMARTdb), which is an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, covering multi-omics, multi-species, and multi-stage data. We have curated and analyzed single-cell transcriptome and epigenome data of over 2.0 million cells from 6 species across whole lifespan. A series of powerful functionalities are provided, such as “Query gene expression”, “DIY expression plot”, “DNA methylation plot”, and “Epigenome browser”. With SMARTdb, we found that the male germ-cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may regulate the specific expression pattern of RPL39L collectively in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":null,"pages":null},"PeriodicalIF":11.5000,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics, Proteomics & Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gpbjnl/qzae005","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here we introduce the single-cell multi-omics atlas of reproduction (SMARTdb), which is an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, covering multi-omics, multi-species, and multi-stage data. We have curated and analyzed single-cell transcriptome and epigenome data of over 2.0 million cells from 6 species across whole lifespan. A series of powerful functionalities are provided, such as “Query gene expression”, “DIY expression plot”, “DNA methylation plot”, and “Epigenome browser”. With SMARTdb, we found that the male germ-cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may regulate the specific expression pattern of RPL39L collectively in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.

查看原文本刊更多论文

SMARTdb：用于探索生殖医学单细胞多组学数据的集成数据库

摘要近年来，单细胞多组学测序技术大大加快了生殖研究的步伐，数据量也在持续增长。然而，对于湿实验室研究人员来说，利用这些数据资源是一项挑战。目前迫切需要一个探索生殖相关单细胞多组学数据的综合平台。我们在此介绍生殖单细胞多组学图谱（SMARTdb），它是一个用于探索生殖发育、衰老和疾病分子动态的综合性、用户友好型平台，涵盖了多组学、多物种和多阶段数据。我们已经整理并分析了来自 6 个物种、跨越整个生命周期的 200 多万个细胞的单细胞转录组和表观基因组数据。它提供了一系列强大的功能，如 "查询基因表达"、"DIY表达图谱"、"DNA甲基化图谱 "和 "表观基因组浏览器"。通过SMARTdb，我们发现RPL39L和RPL10L的雄性生殖细胞特异性表达模式在人类和其他模式动物之间是保守的。此外，DNA 低甲基化和开放染色质可能共同调控 RPL39L 在雄性和雌性生殖细胞中的特异性表达模式。总之，SMARTdb 是一个功能强大的平台，可以方便地进行数据挖掘，并获得有关生殖发育、衰老和疾病的新见解。SMARTdb 可在 https://smart-db.cn 公开获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

14.30

自引率

4.20%

发文量

844

审稿时长

61 days

期刊介绍： Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.