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Links from GEO DataSets

Items: 20

1.

Chromatin Loops Associated with Active Genes and Heterochromatin Shape Rice Genome Architecture for Transcriptional Regulation

(Submitter supplied) We systematically analyze the basic features of chromatin interaction mediated by RNAP2, H3K4me3 and H3K9me2. All interactions further aggregated into higher-order clusters and modular interacting domains with distinct genomic and transcriptional properties. Together, our strategy provides hierarchical and modular 3D genome architecture for transcription regulation in rice.
Organism:
Oryza sativa Indica Group
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26667
12 Samples
Download data: BED
Series
Accession:
GSE131202
ID:
200131202
2.

The ortholog of DDM1 is mainly required for CHG and CG methylation of heterochromatin and is involved in DRM2-mediated CHH methylation that targets mostly genic regions of the rice genome

(Submitter supplied) OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome
Organism:
Oryza sativa Japonica Group
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:
GPL13834
17 Samples
Download data: BAM, BW, CSV, GFF, WIG, XLS
Series
Accession:
GSE81436
ID:
200081436
3.

Integrative analysis of reference epigenomes in rice

(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
Series
Accession:
GSE142570
ID:
200142570
4.

Integrative analysis of reference epigenomes in rice [ChIP-reChIP-seq]

(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
Series
Accession:
GSE142569
ID:
200142569
5.

Integrative analysis of reference epigenomes in rice [BiSulfite-seq]

(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
Series
Accession:
GSE142568
ID:
200142568
6.

Integrative analysis of reference epigenomes in rice [FAIRE-seq]

(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
Series
Accession:
GSE142501
ID:
200142501
7.

Integrative analysis of reference epigenomes in rice [RNA-seq]

(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
Series
Accession:
GSE142470
ID:
200142470
8.

Integrative analysis of reference epigenomes in rice [ChIP-seq]

(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
Series
Accession:
GSE142462
ID:
200142462
9.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [BiSulfite-seq]

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...
Organism:
Oryza sativa
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24468
6 Samples
Download data: BW
Series
Accession:
GSE166613
ID:
200166613
10.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice

(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
154 Samples
Download data: BW, TXT
Series
Accession:
GSE143724
ID:
200143724
11.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [FAIRE-seq]

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24468
12 Samples
Download data: BW
Series
Accession:
GSE143723
ID:
200143723
12.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [DAP-seq]

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24468
2 Samples
Download data: BW
Series
Accession:
GSE143722
ID:
200143722
13.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIA-PET]

(Submitter supplied) Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24468
20 Samples
Download data: BEDPE
Series
Accession:
GSE143721
ID:
200143721
14.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIP-Seq]

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24468
98 Samples
Download data: BW
Series
Accession:
GSE143719
ID:
200143719
15.

Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [RNA-Seq]

(Submitter supplied) Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24468
16 Samples
Download data: TXT
Series
Accession:
GSE143718
ID:
200143718
16.

DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin

(Submitter supplied) In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). more...
Organism:
Oryza sativa Japonica Group
Type:
Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13834
3 Samples
Download data: BW
Series
Accession:
GSE108527
ID:
200108527
17.

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

(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
Series
Accession:
GSE111944
ID:
200111944
18.

ATAC-seq profiling of open chromatin with global epigenetic and transcriptional trends in two-line hybrid rice

(Submitter supplied) The transcriptional regulatory switches responsible for the mechanism of fertility conversion in two-line system of hybrid rice remain unclear. Here, we employed the ATAC-seq, combined with H3K9ac and H3K4me2 and gene expression analyses, in a rice PTGMS Line Wuxiang S to delineate an integrative chromatin accessibility profiling to uncover the key new regulatory modules in response to temperature fluctuation, which can provide important hypotheses regarding the mechanisms of fertility conversion. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL13160 GPL23013 GPL24468
28 Samples
Download data: BED, TXT, WIG
Series
Accession:
GSE114090
ID:
200114090
19.

Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

(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
Platform:
GPL19290
16 Samples
Download data: TXT
Series
Accession:
GSE102921
ID:
200102921
20.

Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance [ChIP-seq]

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...
Organism:
Oryza sativa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19290
6 Samples
Download data: TXT
Series
Accession:
GSE102920
ID:
200102920
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