GEO DataSets

(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; Oryza sativa Japonica Group x Oryza sativa Indica Group; Oryza sativa Japonica Group; Oryza sativa Indica Group x Oryza sativa Japonica 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nasonia vitripennis x Nasonia giraulti

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL21060

8 Samples

Download data: TXT

(Submitter supplied) Wasps of the genus Nasonia are non-social parasitoids that are emerging as a model for studies of epigenetic processes in insects. To study the transmission pattern of DNA methylation and changes of methylation during species divergence, we scored genome-wide methylation and allele-specific methylation (ASM) percentages at single CpG level in both parental and reciprocal F1s of Nv and Ng. These closely related cross-fertile species are genetically tractable and inbred in nature, allowing accurate estimation of ASM. more...

Organism:

Nasonia vitripennis x Nasonia giraulti

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21060

2 Samples

Download data: TXT

(Submitter supplied) We quantified genome-wide total and allele-specific expression in two non-social parasitoids wasp species Nasonia vitripennis and Nasonia giraulti and their reciprocal F1 hybrids. No parent-of-origin effect in allelic expression was found for >8,000 informative genes, suggesting lack of genomic imprinting in adult Nasonia. Gene expression divergence between Nv and Ng could be attributed to both significant cis- and trans- regulatory changes during evolution.

Organism:

Nasonia vitripennis x Nasonia giraulti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21060

6 Samples

Download data: TXT

(Submitter supplied) We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome, of which nearly 68% were represented in R9308 versus Xieqingzao B by CT and GA SNPs. This may indicate that DNA methylation, a heritable epigenetic mark, exists in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during at least one stage, suggesting that trans effects may mediate most transcriptional differences in hybrid offspring. more...

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

12 Samples

Download data: TXT

(Submitter supplied) Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. These changes in DNA methylation and the associated changes in small RNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

38 Samples

Download data: CSV, TXT, WIG

(Submitter supplied) Heterosis is a phenomenon that hybrids exhibit superior performance relative to the parental phenotypes. However, most studies focused on aboveground agronomic traits. Thus, systematic investigation on root heterosis, particularly at reproductive stage in rice is needed to be carried out. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis study.Using the Illumina HiSeq 2000 platform, the root transcriptome of a super-hybrid rice Xieyou9308 and its parents were analyzed at tillering and heading stages. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

12 Samples

Download data: TXT

(Submitter supplied) The heterotic hybrid offspring of Arabidopsis accessions C24 and Landsberg erecta have altered methylomes. Changes occur most frequently at loci where parental methylation levels are different. There are context-specific biases in the non-additive methylation patterns with mCG generally increased and mCHH decreased relative to the parents. These changes are a result of two main mechanisms, Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM), where the methylation level of one parental allele alters to resemble that of the other parent. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: BSP, TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL9062

40 Samples

Download data: BOWTIE, MAP

(Submitter supplied) Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

12 Samples

Download data: MAP

(Submitter supplied) Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

12 Samples

Download data: BOWTIE

(Submitter supplied) Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

16 Samples

Download data: MAP

(Submitter supplied) High-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified at CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL23013

12 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL23157 GPL28290

490 Samples

Download data: TXT

(Submitter supplied) A large number of epiHybrids families were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28290

74 Samples

Download data: CSV

(Submitter supplied) WGreS of 2 male sterile Columbia lines (msCol)

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL23157

2 Samples

Download data: VCF

(Submitter supplied) WGBS of 169 ddm1-derived epiRILs 169 ddm1-derived epigenetic recombinant inbred lines (epiRILs) were obtained from the Versailles Arabidopsis Stock center of INRA (http://publiclines.versailles.inra.fr/) and they were propagated in a fully automatic phenotyping facility for small plants at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Whole Genome Bisulphite Sequencing was performed at the Beijing Genome Institute.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

169 Samples

Download data: TXT

(Submitter supplied) WGBS of 169 ddm1-derived epiHybrids and their corresponding maternal msCol lines A large number of epiHybrids families (169 epiHybrids) were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

171 Samples

Download data: TXT

(Submitter supplied) A large number of epiHybrids families were generated by crossing a male sterile maternal plant of the Columbia accession (msCol) to different paternal ddm1-2 derived epiRILs (Johannes et al., 2009)

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28290

74 Samples

Download data: CSV