GEO DataSets

(Submitter supplied) To understand the evolution of imprinting mechanisms in the rice species Oryza sativa, we analyzed DNA methylation, transcription and small RNA expression in embryo and endosperm. Cultivars chosen to represent the genetic diversity of cultivated Oryza sativa comprised Nipponbare and Kitaake of the japonica subspecies, and IR64 and 93-11 cultivars of the indica subspecies. While imprinted expression is generally conserved among rice cultivars, approximately 10% of imprinted genes show imprinting divergence across the four cultivars. more...

Organism:

Oryza sativa

Type:

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

Platforms:

GPL19290 GPL13160

74 Samples

Download data: GFF

(Submitter supplied) We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. more...

Organism:

Oryza sativa

Type:

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

Platforms:

GPL13160 GPL15432

16 Samples

Download data: GFF

(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) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27660

2 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: BIGWIG

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27660

4 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Other

Platform:

GPL27660

2 Samples

Download data: FA

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL27660

14 Samples

Download data: BIGWIG, FA, TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19290 GPL27660

6 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm development.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT

(Submitter supplied) Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm development.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: FA

(Submitter supplied) Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). more...

Organism:

Zea mays

Type:

Methylation profiling by genome tiling array

Platform:

GPL13499

6 Samples

Download data: PAIR, 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) 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) Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which contrasts with findings from Arabidopsis. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24468 GPL19290

15 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17639 GPL34120 GPL26208

40 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26208

2 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently e v olv ed in the en- dosperm of flo w ering plants and the placenta of mammals—tissues crucial f or nurturing embry os. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct in v estigations of the impact of de no v o TE transposition on genomic imprinting remain scarce. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26208

8 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34120

24 Samples

Download data: BW