Processed RNA expression count data from Groen et al.: The strength and pattern of natural selection on rice gene expression

We assessed transcriptome variation in populations of 216 accessions of rice, <em>Oryza sativa</em>, which represented all major varietal groups including indica and japonica. During the 2016 Philippines dry season the accessions were planted in triplicate (with two accessions planted in triplicate three times as replicated checks) in identical alpha-lattice layouts of 660 plots in two fields: a continuously wet paddy, and a field where plants were exposed to intermittent drought in the vegetative and reproductive stages. We measured transcript levels in leaf blades of 50-day-old plants at 33 days after seedling transplant, and 17 days after withholding water in the dry field, using a liquid automation-based 3’ mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library. Raw sequencing data are available at the SRA in BioProject accession number PRJNA588478. A key to the raw sequencing data in this BioProject can be found in the metadata of the processed RNA expression count data here.本研究评估了216份水稻（*Oryza sativa*）的群体转录组（transcriptome）变异，所用种质涵盖包括籼稻（indica）、粳稻（japonica）在内的所有主要栽培稻类群。2016年菲律宾旱季，我们将所有种质设置三次重复种植，其中2份种质额外增设三次重复作为重复对照，两块试验场均采用包含660个小区的统一α格子设计（alpha-lattice）布局：一块为持续淹水稻田，另一块在植株营养生长与生殖生长阶段施加间歇性干旱胁迫。本研究采用基于液体自动化的3' mRNA测序（3’ mRNA-seq）定量方法，分别在秧苗移栽后33天（此时植株生长至50日龄）采集50日龄植株的叶片样本，以及干旱处理田块停水17天后的叶片样本，检测其转录本水平。样本以每批次96个的规格进行混样建库。原始测序数据可通过登录号为PRJNA588478的生物项目（BioProject），在序列读取档案（Sequence Read Archive, SRA）中获取。本生物项目中原始测序数据的详细说明索引，可从此处提供的处理后RNA表达计数数据的元数据中获取。