Study : Oryza sativa cultivar:Nipponbare Raw sequence reads

Identification

• Name: Oryza sativa cultivar:Nipponbare Raw sequence reads
• Identifier: dXJuOkVWQS9zdHVkeS9QUkpOQTQwMTUyMw==
• Data link: Link to this study on EBI European Nucleotide Archive
• Description: We utilize Structure-seq method to reveal the landscape of in vivo RNA structurome in rice. We apply dimethyl sulfate (DMS) to Oryza sativa L. ssp. japonica cv. Nipponbare seedlings. Two independent biological replicates are generated for both (-) and (+) DMS treatment. Two round poly(A) selection have been performed. The four Structure-seq libraries are sequenced on Illumina Hiseq 4000 sequencing platform for 50bp single-end sequencing. We achieved more than 500 million total reads. Nearly 90% reads are mapped to transcriptomic reference. Two well-correlated biological replicates are merged for further analysis. More than 95% of mapped reads are mRNAs. The adenosines and cytidines before the reverse transcription stops are highly enriched in (+) DMS libraries. There are 30,848 transcripts covered with more than 1 read/nt in (+) DMS libraries. The Structure-seq reactivity is highly and positively correlated to conventional gel electrophoresis reactivity, which indicates Structure-seq can provide similar structural information to classical technology. Thus, we have successfully generated in vivo Structure-seq libraries with high quality and depths in rice.
• Data files: SRR6010250; SRR6010251; SRR6010248; SRR6010249