biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsGiwon KimIllumina NovaSeq 6000RNA-seq of coding RNAOryza sativa Japonica GroupOryza sativa Japonica Grouphttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16817This dataset contains RNA-seq profiles of rice flag leaves collected at five developmental and senescence-associated stages, designated as BFL, FL, 1W_AFL, 3W_AFL, and 5W_AFL. The experiment was designed to characterize transcriptomic changes associated with the progression of natural leaf senescence in rice. Two biological replicates were analyzed for each stage, and each sample was sequenced using paired-end RNA sequencing. These data can be used to identify stage-preferential gene expression patterns and regulatory pathways associated with post-heading flag leaf senescence.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was extracted from frozen rice flag-leaf tissue using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed prior to library preparation, and only high-quality RNA samples were used for sequencing. Extracted RNA was used for transcriptome analysis of wild-type flag leaves collected at the five developmental stages.Sequencing - Sequencing libraries were analyzed on an Illumina NovaSeq 6000 platform to generate paired-end RNA-seq reads. Two biological replicates were sequenced for each developmental stage. The resulting raw sequence data were used for downstream quality control, read trimming, genome alignment, and differential gene expression analysis.Sample Collection - Flag leaves were collected from wild-type rice plants (Oryza sativa L. cv. Dongjin) grown under field conditions at Kyung Hee University, Yongin, Republic of Korea. Samples were harvested at five reproductive stages spanning natural senescence progression: one week before heading, heading, one week after heading, three weeks after heading, and five weeks after heading. At each stage, flag leaves were sampled based on panicle developmental status to ensure consistent stage definition. Two independent biological replicates were collected for each stage. All samples were immediately frozen in liquid nitrogen after harvest and stored at -80°C until RNA extraction.Library Construction - Strand-specific poly(A)+ RNA-seq libraries were constructed from high-quality total RNA using the TruSeq Stranded mRNA Library Preparation Kit (Illumina), following the manufacturer’s protocol. Briefly, polyadenylated RNA was enriched from total RNA, fragmented, and reverse-transcribed to generate first- and second-strand cDNA. After end repair, adapter ligation, and PCR amplification, the final libraries were subjected to sequencing.Growth Protocol - Rice seeds (Oryza sativa L. cv. Dongjin) were surface-sterilized with 50% sodium hypochlorite and germinated on half-strength Murashige and Skoog medium for 7 days at 28/22°C (day/night) under continuous light. Seedlings were transferred to soil in a greenhouse for acclimation and subsequently transplanted to a paddy field at Kyung Hee University, Yongin, Republic of Korea, where plants were cultivated under natural field conditions with standard agronomic management.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesGiwon KimXu JiangYo-Han YooWoo-Jong HongKi-Hong JungfalseTime-course RNA-seq analysis of rice flag leaves across senescence-associated developmental stagesThis dataset contains RNA-seq profiles of rice flag leaves collected at five developmental and senescence-associated stages, designated as BFL, FL, 1W_AFL, 3W_AFL, and 5W_AFL. The experiment was designed to characterize transcriptomic changes associated with the progression of natural leaf senescence in rice. Two biological replicates were analyzed for each stage, and each sample was sequenced using paired-end RNA sequencing. These data can be used to identify stage-preferential gene expression patterns and regulatory pathways associated with post-heading flag leaf senescence.2026-04-05T00:00:00Z2026-04-05T01:01:00.462Z2026-03-27T13:45:57.582ZE-MTAB-16817ERP191479EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184