Project description:This SuperSeries is composed of the following subset Series: GSE26610: DNase I hypersensitive sites in two tissues of rice GSE26733: ChIP-seq to identify the positions of three histone modifications in the rice genome Refer to individual Series
Project description:The histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could eThe histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could enhance gene transcription involved in stress-responsive gene expression. The physiological and molecular mechanisms underlying plant responses to insects are being increasingly studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of transcription of hidden genes in plants damaged by insects remain largely unknown. In current study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-seq). RNA-seq data revealed that 3269 and 4609 genes were up-regulated at 3 h and 12 h after infestation with FAW, respectively. ChIP-Seq analysis revealed 1617 and 2617 genes modified by H3K9ac in rice infested with FAW at 3 h and 12 h, respectively, and H3K9ac was mainly enriched in the transcription start sites of genes.
Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing.
Project description:IDS1 is a rice AP2-type transcription factor with transcritpional repression activity. To understand how IDS1 regulate rice salt tolerance, the ChIP-seq experiments were performed to identify IDS1 binding site in globle genomic level. The two-weeks-old rice seedlings were lysated and sonificated and IDS1-DNA complexes were immune precipated with myc-antibody and protein A beads. The purified DNA samples were used to construct sequencing libraries and sequenced with Illumina. The data were then analyzed with bio-informatic tools.
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected
Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected control and 2 hour were mixed and hybridized with chip besides control and twenty four hours were mixed and hybridized with another chip. Both chips were performed in duplicate
Project description:In order to identify new miRNAs, NAT-siRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. Totally three sets of small RNAs, which were obtained under normal condition as well as salt and drought stress conditions