Nucleic Acids Research,20 November,2025,DOI：https://doi.org/10.1093/nar/gkaf1132

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

Hongjie Liu,Yongsan Yang,Xin Le,Kai Gao,Jingjia Liu,Youfen Fan,Xiaoxi Zeng,Runsheng Chen,Jianjun Zheng,Yi Zhao

Abstract

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.

文章链接：https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1132/8328556#supplementary-data