Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Danio rerio

PROVIDER: GSE97257 | GEO | 2017/06/08

SECONDARY ACCESSION(S): PRJNA381094

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq.

Project description:Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent-activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-seq of nuclei from Tg(fli1a:egfp)y1 transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications. Comparison of ATAC-seq from GFP-positive and -negative nuclei identified more than 5,000 open elements specific to endothelial cells. These elements flanked genes functionally important for vascular development and that displayed endothelial-specific gene expression. Importantly, a majority of tested elements drove endothelial gene expression in zebrafish embryos. Thus, FANS-assisted ATAC-seq using transgenic zebrafish embryos provides a robust approach for genome-wide identification of active tissue-specific enhancer elements.

| S-EPMC5562042 | biostudies-literature

FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers [ATAC-seq]

Project description:Fluorescence-Activated Nuclei Sorting (FANS)-assisted Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.

2017-06-08 | GSE97255 | GEO

FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers [RNA-seq]

Project description:This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.

2017-06-08 | GSE97256 | GEO

FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers

Project description:FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers

| PRJNA381094 | ENA

Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension

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

2020-03-12 | GSE126325 | GEO

H3K18la marks active tissue-specific enhancers

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

2022-09-14 | GSE195860 | GEO

A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-04-07 | E-GEOD-71327 | biostudies-arrayexpress

Short DNA sequence patterns accurately identify broadly active human enhancers.

Project description:BACKGROUND:Enhancers are DNA regulatory elements that influence gene expression. There is substantial diversity in enhancers' activity patterns: some enhancers drive expression in a single cellular context, while others are active across many. Sequence characteristics, such as transcription factor (TF) binding motifs, influence the activity patterns of regulatory sequences; however, the regulatory logic through which specific sequences drive enhancer activity patterns is poorly understood. Recent analysis of Drosophila enhancers suggested that short dinucleotide repeat motifs (DRMs) are general enhancer sequence features that drive broad regulatory activity. However, it is not known whether the regulatory role of DRMs is conserved across species. RESULTS:We performed a comprehensive analysis of the relationship between short DNA sequence patterns, including DRMs, and human enhancer activity in 38,538 enhancers across 411 different contexts. In a machine-learning framework, the occurrence patterns of short sequence motifs accurately predicted broadly active human enhancers. However, DRMs alone were weakly predictive of broad enhancer activity in humans and showed different enrichment patterns than in Drosophila. In general, GC-rich sequence motifs were significantly associated with broad enhancer activity, and consistent with this enrichment, broadly active human TFs recognize GC-rich motifs. CONCLUSIONS:Our results reveal the importance of specific sequence motifs in broadly active human enhancers, demonstrate the lack of evolutionary conservation of the role of DRMs, and provide a computational framework for investigating the logic of enhancer sequences.

| S-EPMC5512948 | biostudies-literature

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-23 | E-GEOD-43103 | biostudies-arrayexpress

Histone H3K27ac separates active from poised enhancers and predicts developmental state

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

2010-10-31 | GSE24165 | GEO