GEO DataSets

(Submitter supplied) The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL9147

24 Samples

Download data: BED, TAR

(Submitter supplied) The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9141

46 Samples

Download data: TXT

(Submitter supplied) We present high-resolution maps of DNA methylation and H3K4 di- and tri-methylation of two entire chromosomes and two fully sequenced centromeres in rice shoots and cultured cells. Most transposable elements have highly methylated DNA but no H3K4 methylation whereas over half of protein-coding genes have both methylated DNA and di- and/or tri-methylated H3K4. Methylation of DNA but not H3K4 correlates with suppressed transcription. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platforms:

GPL6285 GPL6286

32 Samples

Download data: TXT

(Submitter supplied) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL9141

14 Samples

Download data: BED, FA, TXT

(Submitter supplied) We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL13160

5 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL24468

513 Samples

Download data: BW, TXT

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

4 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24468

38 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

58 Samples

Download data: BW

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24468

58 Samples

Download data: TXT

(Submitter supplied) Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24468

355 Samples

Download data: BW

(Submitter supplied) We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL24468 GPL19290

10 Samples

Download data: BED, TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9316

7 Samples

Download data: TXT

(Submitter supplied) The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, while the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

9 Samples

Download data: CSV

(Submitter supplied) Identification of all expressed transcripts in a sequenced complex genome is technically challenging, but essential for systems biology and genome analysis. We used the transcriptional profiling technology called ‘massively parallel signature sequencing’ (MPSS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). A total of 46,971,553 mRNA transcripts from 22 libraries, and 2,953,855 small RNAs from three libraries were sequenced. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platforms:

GPL3777 GPL3776

21 Samples

Download data

(Submitter supplied) We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: BED, TXT

(Submitter supplied) The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

368 Samples

Download data: TXT

(Submitter supplied) Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18525

4 Samples

Download data: TXT

(Submitter supplied) This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring.

Organism:

Oryza sativa Indica Group x Oryza sativa Japonica Group; Oryza sativa Japonica Group; Oryza sativa Indica Group; Oryza sativa Japonica Group x Oryza sativa Indica Group

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: TXT

(Submitter supplied) We analyzed the transcriptional activity of rice chromosom 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Five organ samples from various developmental stages and cultured cells were examined. Keywords: ordered

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL1722

15 Samples

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