Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

ABSTRACT: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

PROVIDER: PRJNA331156 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3950230_1.fastq.gz	Fastqsanger.gz
	SRR3950230_2.fastq.gz	Fastqsanger.gz
	SRR3950240_1.fastq.gz	Fastqsanger.gz
	SRR3950240_2.fastq.gz	Fastqsanger.gz
	SRR3950300.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 144

Similar Datasets

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [RNA-seq]

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

2016-12-06 | GSE84794 | GEO

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [ChIP-seq]

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

2016-12-06 | GSE84793 | GEO

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [Capture-C]

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

2016-12-06 | GSE84792 | GEO

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.

Project description:Complex regulatory landscapes control the pleiotropic transcriptional activities of developmental genes. For most genes, the number, location, and dynamics of their associated regulatory elements are unknown. In this work, we characterized the three-dimensional chromatin microarchitecture and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq, and RNA-seq in forelimb, hindlimb at three developmental stages, and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains. By combining chromatin marks and interaction peaks, we annotated more than 1000 putative limb enhancers and their associated genes. Moreover, the analysis of chromatin interactions revealed two regimes of chromatin folding, one producing interactions stable across tissues and stages and another one associated with tissue and/or stage-specific interactions. Whereas stable interactions associate strongly with CTCF/RAD21 binding, the intensity of variable interactions correlates with changes in underlying chromatin modifications, specifically at the viewpoint and at the interaction site. In conclusion, this comprehensive data set provides a resource for the characterization of hundreds of limb-associated regulatory landscapes and a framework to interpret the chromatin folding dynamics observed during embryogenesis.

| S-EPMC5287228 | biostudies-literature

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-12-06 | GSE84795 | GEO

Mus musculus

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [RNA-seq]

| PRJNA331168 | ENA

Mus musculus

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [Capture-C]

| PRJNA331165 | ENA

Mus musculus

Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [ChIP-seq]

| PRJNA331166 | ENA

Stress promotes RNA G-quadruplex folding in human cells

Project description:Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. Here, we showed that the folding of putative rG4s in human cells into rG4 structures was dynamically induced by stress. By using high-throughput dimethylsulfate probing, we identified hundreds of endogenous stress-induced rG4s. Our results demonstrated that stress-induced rG4s were enriched in mRNA 3′-untranslated regions and enhanced mRNA stability. Furthermore, stress-induced rG4 folding was readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in living human cells and suggests suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.

2022-12-15 | GSE200706 | GEO

Transcriptome of Dinoroseobacter shibae under changeing light regimes

Project description:D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken.

2014-07-01 | GSE57164 | GEO