GEO DataSets

(Submitter supplied) The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in theArabidopsis thalianaecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19580 GPL17639 GPL26208

32 Samples

Download data: TSV

(Submitter supplied) In Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1 pathway. To investigate their biological functions we characterized siRNAs in the endosperm and seed coat that were separated by laser capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatio-temporal activity of the NRPD1 pathway on seed development using AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9302 GPL13222 GPL21785

18 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Interspecific hybrids in Arabidopsis result in seed abortion that causes reproductive barrier. To investigate the allelic expression pattern at transcriptome level during early seed abortion stage, we performed RNA-seq analysis in F1 interspecific hybrids with three different ecotypes in A. thaliana as maternal and A. arenosa as paternal and identified MEGs and PEGs. Interestingly, PEGs showed distinct expression pattern in several aspects, compared to MEGs: PEGs showed ecotype-specific expression pattern, suggesting a role for PEGs in ecotype-dependent seed lethality. more...

Organism:

Arabidopsis thaliana x Arabidopsis arenosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16156

4 Samples

Download data: TXT

(Submitter supplied) We report the identification of parent-of-origin specific gene expression in Arabidopsis seeds. F1 hybrid seeds were generated by reciprocally crossing Arabidopsis accessions Col-0 and Bur-0. Seeds were harvested at 4 DAP and total RNA was isolated and analyzed by deep sequencing.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11221

2 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; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

20 Samples

Download data: BEDGRAPH

(Submitter supplied) Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess results in extensive endosperm proliferation without cellularization and eventual seed abortion. We previously showed that loss of the RNA POL IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL17639

10 Samples

Download data: XLSX

(Submitter supplied) Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess results in extensive endosperm proliferation without cellularization and eventual seed abortion. We previously showed that loss of the RNA POL IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL17639

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess results in extensive endosperm proliferation without cellularization and eventual seed abortion. We previously showed that loss of the RNA POL IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: BED, TDF, TXT

(Submitter supplied) Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation. Interestingly, during seed development EIN2 is maternally-expressed in Arabidopsis and maize, but the role of EIN2 in seed development is unknown. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

8 Samples

Download data: TXT

(Submitter supplied) Genetic imprinting is an epigenetic phenomenon that describes unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms including mammals and flowering plants. The function of imprinted genes was rarely reported. We report genome-wide analysis of gene expression, DNA methylation, and small RNAs in the rice endosperm and functional tests of five imprinted genes in seed development using CRISPR/Cas9 editing technology. more...

Organism:

Oryza sativa

Type:

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

Platforms:

GPL19290 GPL13160

14 Samples

Download data: TXT

(Submitter supplied) Seeds are the basis of agriculture, yet their full transcriptional complexity has remained unknown. Here, we employ single-nucleus RNA-sequencing to characterize developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the site of gene imprinting in plants, mediates the relationship between the maternal parent and embryo. We identify new cell types in the chalazal endosperm region, which interfaces with maternal tissue for nutrient unloading. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19580 GPL13222

1664 Samples

Download data: TXT

(Submitter supplied) In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: TXT

(Submitter supplied) Sperm cells represent the male partner that fuses with the egg cell during fertilization in all multi-cellular eukaryotic organisms, and, in flowering plants, is a founder of both embryo and nutritive endosperm. We examined the transcriptome of Oryza sativa ssp. japonica using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated in the paternal gamete. We used microarrays to detail the global program of gene expression in mature pollen and sperm cells at anthesis, which constitutes the stage immediately preceding pollen germination and gamete deposition leading up to fertilization. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

9 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

27 Samples

Download data

(Submitter supplied) Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

5 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: BED, TXT

(Submitter supplied) Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

10 Samples

Download data: TXT

(Submitter supplied) High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col and Ler reciprocal F1 hybrid embryo and endosperm tissue isolated at 6-7 days after pollination to identify imprinted genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: SAM