Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

ABSTRACT: Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

PROVIDER: PRJNA756315 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15530400_1.fastq.gz	Fastqsanger.gz
	SRR15530400_2.fastq.gz	Fastqsanger.gz
	SRR15530401_1.fastq.gz	Fastqsanger.gz
	SRR15530401_2.fastq.gz	Fastqsanger.gz
	SRR15530402_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

Project description:Cleavage sites induced by the EcTopoI G116S M320V topoisomerase mutant were identified in E. coli genome with a single-nucleotide resolution using Topo-Seq.

2022-01-01 | GSE182473 | GEO

Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

Project description:Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq’s exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

2024-08-06 | GSE267149 | GEO

Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

Project description:Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

| PRJNA1109861 | ENA

Genome-wide maps of Topoisomerase IV binding and cleavage sites in E. coli

Project description:We report binding of Topoisomerase IV on the E. coli genome. We report the cleavage sites of Topoisomerase IV on the E. coli genome

2016-04-21 | GSE75641 | GEO

Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

Project description:Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

| PRJNA931747 | ENA

Cleavage mapping in rps3

Project description:Cleavage mapping in rps3

| PRJNA482833 | ENA

Genome-wide mapping of cleavage sites induced by topoisomerase IV in E. coli with a single-nucleotide resolution

Project description:Topo IV cleavage sites induced by ciprofloxacin were identified in the E. coli genome with a single-nucleotide resolution using Topo-Seq.

2023-02-05 | GSE224562 | GEO

Defining Giardia lamblia cleavage sites

Project description:Defining Giardia lamblia cleavage sites

| PRJNA713373 | ENA

Fluoroquinolone-induced gyrase cleavage sites

Project description:Fluoroquinolone-induced gyrase cleavage sites

| PRJNA851452 | ENA

Mapping of genome-wide action sites of topoisomerase IIbeta by a functional ChIP-chip technique (eTIP-tiling array)

Project description:DNA topoisomerase II (topo II) catalyzes a strand passage reaction in that one duplex is passed through a transient brake in another. Completion of late stages of neuronal development depends on the presence of active isoform (topo IIbeta). We identified topo IIbeta action sites on 7 selected genomic regions (about 79 Mb in total), each containing at least one gene that is controlled by topo IIbeta in neuronal differentiation. We used a novel method, etoposide-mediated topoisomerase immunoprecipitation (eTIP), followed by identification of precipitated DNA fragments on genomic tiling arrays. These DNA fragments were first fractionated by concentrated salt prior to the array analysis. The 0.5 M NaCl-released fraction was analyzed as P2 and the salt-resistant fraction wad analyzed as P1. The genomic DNA fractions from the immunoprecipitate (P1 or P2) were co-hybridized with a reference DNA isolated from the input of immunoprecipitation.

2010-05-15 | E-GEOD-13145 | 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