Rice Expression Database (RED) 2.0: an updated rice database integrating diverse RNA expression profiles based on the telomere-to-telomere reference genome

Abstract

Rice Expression Database (RED) is a rice gene expression database derived from large-scale RNA-seq data across different tissues and experimental conditions. Here, we present RED 2.0 (https://ngdc.cncb.ac.cn/red) with significant updates and enhancements. Specifically, RED 2.0 contains 357 projects covering 6471 bulk RNA-seq experiments across 18 tissues and 78 single-cell RNA-seq experiments comprising 984 495 cells. All projects are further manually curated and grouped into diverse biological contexts, including abiotic stress, biotic stress, hormone, development, genotype, and anatomy. Notably, based on the telomere-to-telomere assembly of the Nipponbare genome, RED 2.0 incorporates comprehensive expression profiles for 57 359 protein-coding genes (67 818 transcripts), 16 522 long non-coding RNA genes (47 396 transcripts), and 79 007 circular RNAs. In addition, it is equipped with online tools for differential expression analysis, functional enrichment analysis, co-expression network construction, and genome browser. Collectively, RED 2.0 provides a comprehensive expression landscape for both coding and non-coding genes across diverse conditions, serving as an important resource for rice functional genomics and molecular breeding.