NONCODE v7.0: updated lncRNA resource integrating scRNA-seq data encompassing immune baseline, development, and disease

doi:10.1093/nar/gkaf1132

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	NONCODE v7.0: updated lncRNA resource integrating scRNA-seq data encompassing immune baseline, development, and disease
	Liu, Hongjie 1,2,3; Yang, Yongsan 4; Le, Xin 5; Gao, Kai 6; Liu, Jingjia 5; Fan, Youfen 5; Zeng, Xiaoxi 4; Chen, Runsheng 3,7; Zheng, Jianjun 1; Zhao, Yi 2,3
	2025-11-20
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
页码	8
摘要	The rapid advancement of single-cell multi-omics technologies, typified by single-cell RNA sequencing (scRNA-seq), has provided systematic methodologies for dissecting gene expression heterogeneity within cell populations. However, long noncoding RNAs (lncRNAs) research is hindered by a lack of databases covering diverse tissues, disease contexts, and integrated multi-dimensional single-cell annotations. To address this gap, we updated NONCODE v7.0 (available at https://v7.noncode.org/) through the integration of scRNA-seq data, enabling systematic analysis of lncRNA expression. NONCODE v7.0 incorporates 2061 human scRNA-seq samples from 229 datasets, covering a spectrum of 6 categories, with 3 core ones including Physiological Control as an immune baseline, Physiological Development, and Pathological Disease. Following standardized quality control and processing, the database encompasses 14 million high-quality cells and annotates 94 843 lncRNAs (98.5% of human lncRNAs in NONCODE v6.0). Furthermore, we extended the database through the integration of single-cell-tailored functional modules, encompassing data query and retrieval, interactive visualization (including cell composition, UMAP/t-SNE clustering, marker gene heatmaps, and lncRNA expression profiles), and comparative analysis functionalities. The analytical module facilitates the identification of cell-type-specific differentially expressed (DE) lncRNAs across distinct disease states, thus establishing a foundational resource platform to facilitate the advancement of downstream functional investigations into lncRNAs.
DOI	10.1093/nar/gkaf1132
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:001618167300001
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/43062
专题	中国科学院计算技术研究所
通讯作者	Chen, Runsheng; Zheng, Jianjun; Zhao, Yi
作者单位	1.Ningbo 2 Hosp, Dept Radiol, 41 Xibei Str, Ningbo 315010, Zhejiang, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Sichuan Univ, West China Hosp, West China Biomed Big Data Ctr, Chengdu 610041, Sichuan, Peoples R China 5.Ningbo 2 Hosp, Dept Burn, 41 Northwest St, Ningbo 315010, Zhejiang, Peoples R China 6.Ningbo 2 Hosp, Dept Resp & Crit Care Med, Ningbo 315010, Zhejiang, Peoples R China 7.Chinese Acad Sci, Inst Biophys, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Liu, Hongjie,Yang, Yongsan,Le, Xin,et al. NONCODE v7.0: updated lncRNA resource integrating scRNA-seq data encompassing immune baseline, development, and disease[J]. NUCLEIC ACIDS RESEARCH,2025:8.
APA	Liu, Hongjie.,Yang, Yongsan.,Le, Xin.,Gao, Kai.,Liu, Jingjia.,...&Zhao, Yi.(2025).NONCODE v7.0: updated lncRNA resource integrating scRNA-seq data encompassing immune baseline, development, and disease.NUCLEIC ACIDS RESEARCH,8.
MLA	Liu, Hongjie,et al."NONCODE v7.0: updated lncRNA resource integrating scRNA-seq data encompassing immune baseline, development, and disease".NUCLEIC ACIDS RESEARCH (2025):8.