Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DREAM-seq, an endonucleases-assisted mapping of R-loops

ABSTRACT: DREAM-seq, an endonucleases-assisted mapping of R-loops

PROVIDER: PRJNA412545 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6116720.fastq.gz	Fastqsanger.gz
	SRR6116730.fastq.gz	Fastqsanger.gz
	SRR6116740.fastq.gz	Fastqsanger.gz
	SRR6116721.fastq.gz	Fastqsanger.gz
	SRR6116731.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

Project description:DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

2021-02-09 | GSE110477 | GEO

DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

Project description:DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

| PRJNA433837 | ENA

DREAM-seq, an endonucleases-assisted mapping of R-loops

Project description:Genome-wide identification of R-loops almost uniquely relies on antibody based pull-down, a method that shows sequence and structural biases. Here we describe a novel approach – DREAM-seq – centered around the use of endonuclease digestions. Unstimulated and stimulated B cells showed that R-loops are more widespread than anticipated, mostly covering all actively transcribed genes.

2020-09-26 | GSE104413 | GEO

Genome-wide mapping of native G-loops in living cells

Project description:G-quadruplex (G4) are four‑stranded DNA secondary structures that form in guanine‑rich regions of the genome, which can enhance or repress gene expression. An R-loop is a special triple-stranded nucleic acid structure formed when nascent RNA invades double-stranded DNA (dsDNA) during transcription. G-loops are constituted by one or more DNA G4 on one strand and a stable RNA/DNA hybrid on the other. We developed the HepG4-seq for mapping the native G4s and the HBD-seq for mapping native R-loops. We combined the HepG4-seq and HBD-seq to profile the genomic native G-loops, which are regions co-occupied by both native G4s and R-loops, in both HEK293 cells and mouse embryonic stem cells (mESCs).

2024-07-25 | GSE254764 | GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA957458 | ENA

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA1108725 | ENA

Best practices for the visualization, mapping, and manipulation of R-loops

Project description:R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution significantly impacts genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here we review the main existing methodologies underlying R-loop mapping and assess their limitations and the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we offer a possible resolution to the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.

2021-02-24 | GSE158480 | GEO

The DREAM complex functions as conserved master regulator of somatic DNA repair capacities

Project description:Mutations in the DREAM complex induce germline-like gene expression patterns including the increase of multiple mechanisms of DNA repair in the soma of Caenorhabditis elegans. This confers mutants of the DREAM complex resistance to a wide range of DNA damage types during development and aging.

2023-01-31 | PXD033836 | Pride

Genome-wide mapping of native G-loops in living cells

Project description:Genome-wide mapping of native G-loops in living cells

| PRJNA1071642 | ENA

DREAM On, DREAM Off: A Review of the Estrogen Paradox

Project description:DREAM On, DREAM Off: A Review of the Estrogen Paradox

| PRJNA1114009 | ENA