Rice (Oryza sativa) dataset from detailed molecular profiling uncovering dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice coleoptiles under anoxia and re-oxygenation

This dataset originates from research carried out in 2016, published in the paper "Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation." The RNA-seq data generated provides a detailed molecular profile of Oryza sativa enabling the identification of differentially expressed genes and uncovers the essential features for germination and early seedling growth under anoxic conditions.The data provide insights into the molecular responses to oxygen deprivation. An extensive time course was examined, from dry seeds to germinating embryos (24 h) and up to 4-day-old rice coleoptiles, as well as coleoptiles collected from seedlings grown for 3 days under anoxic conditions and transferred to air for one day.In rice, germination and seedling development can progress in both the presence and absence of oxygen. While the transcriptomic responses to anaerobic conditions, found using microarrays, have revealed common responses, even across kingdoms, these alone are not sufficient for altering tolerance to anaerobic conditions. An in-depth study was undertaken which resulted in data creation from several time points during germination and in the rice coleoptile using RNA-seq analyses.

本数据集源自2016年开展的一项研究，相关成果发表于论文《缺氧与复氧条件下水稻（Oryza sativa）萌发过程及发育胚芽鞘中转录组与表观基因组的动态快速变化》。本次研究生成的RNA测序（RNA-seq）数据为水稻提供了详尽的分子特征图谱，可用于鉴定差异表达基因，并揭示了缺氧条件下水稻萌发及幼苗早期生长的关键特征。该数据集为解析植物对缺氧胁迫的分子应答机制提供了重要见解。研究覆盖了完整的时间进程样本：从干燥种子、萌发胚（24小时）直至4日龄水稻胚芽鞘；同时还包含在缺氧条件下培养3天后，转移至正常空气环境中培养1天的幼苗胚芽鞘样本。水稻的萌发与幼苗发育可在有氧及无氧环境下均顺利完成。此前利用微阵列（microarray）技术开展的厌氧条件转录组响应研究已发现，即便跨生物界也存在共通的厌氧应答模式，但仅靠此类应答不足以调控植物对厌氧环境的耐受性。本研究通过深入系统的分析，利用RNA-seq技术对水稻萌发过程及胚芽鞘发育的多个时间点进行测序，最终生成了本数据集。