Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

ORGANISM(S): Oryza sativa

PROVIDER: GSE142569 | GEO | 2020/04/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description: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. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

2020-04-25 | GSE142568 | GEO

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

2020-04-25 | GSE142501 | GEO

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

2020-04-25 | GSE142462 | GEO

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

2020-04-25 | GSE142470 | GEO

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-reChIP]

Project description:We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

2021-01-31 | GSE143284 | GEO

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

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

| PRJNA597478 | ENA

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS]

2021-01-31 | GSE143285 | GEO

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

2021-01-31 | GSE143286 | GEO

Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-seq]

2021-01-31 | GSE143283 | GEO

Integrative analysis of 111 reference human epigenomes.

Project description:The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

| S-EPMC4530010 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data