Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ISDH-seq: a robust methodology for profiling and characterization of open chromatin

ABSTRACT: ISDH-seq: a robust methodology for profiling and characterization of open chromatin

PROVIDER: PRJNA988012 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32604967_1.fastq.gz	Fastqsanger.gz
	SRR32604967_2.fastq.gz	Fastqsanger.gz
	SRR32604968_1.fastq.gz	Fastqsanger.gz
	SRR32604968_2.fastq.gz	Fastqsanger.gz
	SRR32604969_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 22

Similar Datasets

ISDH-seq: a robust methodology for profiling and characterization of open chromatin

Project description:We present in situ DNase I hypersensitivity sequencing (ISDH-seq), a novel methodology for genome-wide open chromatin characterization in plants, which can be applicable to 100-200K nuclei. Compared to conventional DNase-seq and ATAC-seq applied to the same rice tissues, ISDH-seq detects 72% and 120% more open chromatin sites (OCSs), respectively. ISDH-specific OCSs exhibit unique epigenetic signatures: hypomethylation, co-enrichment with H3K27me3, and strong spatial chromatin interaction associations.ISDH-seq overcomes method-specific biases in OCS detection, expands the plant regulatory genome atlas, and offers cross-species applicability. This technology provides critical insights into noncoding regulatory mechanisms and their biological implications in plant genomes.

2025-05-01 | GSE235900 | GEO

ISRH-seq: a sensitive and robust methodology for R-loop profiling

Project description:ISRH-seq: a sensitive and robust methodology for R-loop profiling

| PRJNA971645 | ENA

ISRH-seq: a sensitive and robust methodology for R-loop profiling

Project description:R-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an antibody-independent approach for strand-specific mapping of R-loops. After conducting a parallel comparison with DRIP-seq, we found that ISRH-seq can identify more R-loop peaks with the same sequencing depth. Moreover, ISRH- and DRIP-specific R-loops had distinct genomic and epigenetic features, exhibited distinct relationships with expression of overlapping genes, and functional divergence. Importantly, we found that ISRH-seq can be scalable down to 250-100ng DNA input, indicative of a robust and sensitive high-throughput methodology. In addition, it can be applied for R-loop profiling under stress conditions. Thus, our study provides a valuable orthogonal methodology for comprehensive profiling of R-loops in plants. It could be easily adapted to other non-plant systems, especially for these biologically important tissues or cell types with limited cell numbers, thereby advancing understanding of R-loop biology.

2024-05-16 | GSE232347 | GEO

Characterization of open chromatin sensitive to actin polymerization using DSP-MNase-DNA-seq

Project description:Characterization of open chromatin sensitive to actin polymerization using DSP-MNase-DNA-seq

| PRJNA1080193 | ENA

Open chromatin maps of genetically different yeast strains

Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. For a quantitative getic analysis of chromatin regulation, we generated open chromatin maps of 100 yeast samples including the parental strains (BY and RM, and two replicates for each) and their descendants by using the FAIRE-seq technique Open chromatin in two parental strains and 94 segregants of their crossing

2012-11-02 | E-GEOD-33466 | biostudies-arrayexpress

NicE-C efficiently reveals open chromatin associated chromosome interactions at high resolution

Project description:Enhancer-promoter communication is known to regulate spatiotemporal gene expression. Here, we present NicE-C, a method that leverages nicking enzyme mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of chromatin interactions among open chromatin regions (e.g., between enhancers and promoters). Demonstrating its application utility, NicE-C revealed dynamic enhancer-promoter interactions associated with gene expression changes after TNFɑ stimulation in HeLa cells and during aging process in mice kidney.

2022-01-18 | GSE176066 | GEO

Robust 4C-seq data analysis to screen for regulatory DNA interactions

Project description:Regulatory DNA elements can control expression of distant genes via physical interactions. Here, we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using Chromosome Conformation Capture combined with high-throughput sequencing (4C-seq) data. Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation. A high resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline was applied to several viewpoints in four genomic loci (the well-characterized alpha-globin and beta-globin loci, and the novel Oct4 and Satb1 loci), allowing robust detection of physical interactions between regulatory DNA elements.

2012-09-04 | E-GEOD-40420 | biostudies-arrayexpress

iPSC ATAC-seq open chromatin

Project description:Mapping open chromatin in iPSCs derived from beta-cells

| PRJEB21856 | ENA

Robust 4C-seq data analysis to screen for regulatory DNA interactions

2012-09-04 | GSE40420 | GEO

Open chromatin profiling in the U2OS cell

Project description:In order to identify the open chromatin profiles in the U2OS cell, ATAC-seq technology was used to determine the accessible chromatin landscape in U2OS cell.

2023-06-01 | E-MTAB-12294 | 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