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

RED 2.0 compiles 357 projects with 6,471 bulk RNA-seq experiments across 18 tissues and 78 single-cell RNA-seq experiments totaling 984,495 cells for rice functional genomics.

• Why it matters: A unified, curated resource is needed to integrate diverse rice RNA expression profiles across tissues and experimental contexts for coding and non-coding genes.
• What they did: RED 2.0 manually curates projects grouped into abiotic/biotic stress, hormone, development, genotype, and anatomy, and maps expression to the telomere-to-telomere Nipponbare assembly.
• The result: It provides expression profiles for 57,359 protein-coding genes (67,818 transcripts), 16,522 lncRNA genes (47,396 transcripts), and 79,007 circular RNAs, with tools for differential expression, enrichment, co-expression networks, and genome browsing.