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

PROVIDER: PRJNA381094 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5398230_1.fastq.gz	Fastqsanger.gz
	SRR5398230_2.fastq.gz	Fastqsanger.gz
	SRR5398231.fastq.gz	Fastqsanger.gz
	SRR5398232.fastq.gz	Fastqsanger.gz
	SRR5398233.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

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

Danio rerio

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

| PRJNA381095 | ENA

Danio rerio

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

| PRJNA381096 | ENA

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

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

2017-06-08 | GSE97257 | 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

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

H3K18la marks active tissue-specific enhancers

Project description:H3K18la marks active tissue-specific enhancers

| PRJNA802354 | ENA

Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

Project description:Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

| PRJNA531411 | ENA

Transcriptionally active enhancers in human cancer cells

Project description:Transcriptionally active enhancers in human cancer cells

| PRJNA638913 | ENA

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

Project description:Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade. Analysis of 5fC/5caC excision repair-dependent active DNA demethylome by MAB-seq in mouse embryonic stem cells.

2014-11-02 | E-GEOD-62631 | biostudies-arrayexpress

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