Jiang Tiantongfei, Jin Xiaoyan, Gao Yueying, Zhou Weiwei, Yu Jinyang, Li Yongsheng, Xu Juan, Cai Benzhi
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
Department of Pharmacy, The Second Affiliated Hospital, Department of Pharmacology, College of Pharmacy, (The Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), Harbin Medical University, Harbin, 150081, China.
Biomark Res. 2024 Nov 28;12(1):149. doi: 10.1186/s40364-024-00696-5.
Increasing scRNA-seq data in cardiovascular research have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. However, the single-cell transcriptome datasets were dispersed in literature and no resource for cardiovascular systems and diseases. Here, we constructed an organized resource CardioAtlas, which provides comprehensive analysis results for > 1,929,000 cells in 27 human data sets and > 1,088,000 cells in 39 mouse data sets. Through large-scale literature retrieval and manual annotation, we constructed 12 and 15 scRNA-seq reference atlas for common human and mouse cardiovascular systems and diseases, covering 43 and 39 cell types. In particular, CardioAtlas provides five analytic modules, including cell-type prediction, identification of marker genes, functional enrichment analysis, identification of cell-type-specific transcription regulons, and cell-cell communication analysis. In addition, users can upload scRNA-seq data for personalized analysis. CardioAtlas is available at http://bio-bigdata.hrbmu.edu.cn/CardioAtlas . CardioAtlas provides the first comprehensive and well-crafted reference atlas of cardiovascular systems and diseases and describes in detail previously unrecognized cell populations across a large number of humans and mice.
心血管研究中不断增加的单细胞RNA测序（scRNA-seq）数据极大地提升了我们对心血管系统发育以及心血管疾病潜在机制的认识。然而，单细胞转录组数据集分散在文献中，且缺乏针对心血管系统和疾病的资源。在此，我们构建了一个有条理的资源库CardioAtlas，它为27个人类数据集中的>192.9万个细胞以及39个小鼠数据集中的>108.8万个细胞提供了全面的分析结果。通过大规模文献检索和人工注释，我们构建了针对常见人类和小鼠心血管系统及疾病的12个和15个scRNA-seq参考图谱，涵盖43种和39种细胞类型。特别地，CardioAtlas提供了五个分析模块，包括细胞类型预测、标记基因鉴定、功能富集分析、细胞类型特异性转录调控子鉴定以及细胞间通讯分析。此外，用户可以上传scRNA-seq数据进行个性化分析。CardioAtlas可在http://bio-bigdata.hrbmu.edu.cn/CardioAtlas获取。CardioAtlas提供了首个全面且精心制作的心血管系统和疾病参考图谱，并详细描述了大量人类和小鼠中先前未被识别的细胞群体。
