GSE201399
Transcriptome profiling of rice plants in response to 2-Nitroaniline
In order to investigate the roles of ScOYE3, an old yellow enzyme gene from Saccharomyces cerevisiae, in detoxification and phytoremediation of 2-Nitroaniline (2-NA) in rice, we employed the RNA-seq approach to identify differentially expressed genes in 2-NA-treated wild-type (ZH11) rice plants and transgenic (OE1) rice plants overexpressing ScOYE3. Processing of RNA samples on the Illumina HiSeq 4000 system yielded more than 50 million reads, each 100bp in length, encompassing 6.28Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as TPMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized TPMs (padjust<0.05) in comparison analysis. Overall design: RNA-sequencing was carried out using ZH11 and transgenic (OE1) rice seedlings. Total RNA was isolated with Trizol reagent (Invitrogen, USA) from untreated and 2-NA treated two-week-old seedlings of ZH11 and OE1 grown in parallel. Materials from 20 plants of each sample were pooled for RNA isolation.