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

Nucleic Acids Res. 2026 Jan 6;54(D1):D239-D246. doi: 10.1093/nar/gkaf1132.

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.

PMID:41261731 | PMC:PMC12807645 | DOI:10.1093/nar/gkaf1132