Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks and lesions by GLOE-Seq

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

ORGANISM(S): Saccharomyces cerevisiae Homo sapiens

PROVIDER: GSE134225 | GEO | 2020/04/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.

Project description:DNA single-strand breaks (SSBs) are among the most common lesions in the genome, arising spontaneously and as intermediates of many DNA transactions. Nevertheless, in contrast to double-strand breaks (DSBs), their distribution in the genome has hardly been addressed in a meaningful way. We now present a technique based on genome-wide ligation of 3'-OH ends followed by sequencing (GLOE-Seq) and an associated computational pipeline designed for capturing SSBs but versatile enough to be applied to any lesion convertible into a free 3'-OH terminus. We demonstrate its applicability to mapping of Okazaki fragments without prior size selection and provide insight into the relative contributions of DNA ligase 1 and ligase 3 to Okazaki fragment maturation in human cells. In addition, our analysis reveals biases and asymmetries in the distribution of spontaneous SSBs in yeast and human chromatin, distinct from the patterns of DSBs.

| S-EPMC7276987 | biostudies-literature

Preparation and Analysis of GLOE-Seq Libraries for Genome-Wide Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions.

Project description:GLOE-Seq is a next-generation sequencing method for the genome-wide mapping of 3'-OH termini, either resulting from single- or double-strand breaks or introduced by enzymatic conversion of lesions or modified nucleotides. This protocol provides instructions for isolation of genomic DNA from budding yeast or mammalian cells, preparation of libraries for sequencing, and data analysis by the associated computational pipeline, GLOE-Pipe. It is optimized for the Illumina next-generation sequencing platform and can be adapted to intact genomic DNA of any origin. For complete details on the use and execution of this protocol, please refer to Sriramachandran et al. (2020).

| S-EPMC7580242 | biostudies-literature

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [digestion]

Project description:Numerous methods are available for the mapping of DNA lesions ranging from double-strand breaks (DSBs) to incorporated ribonucleotides. We now present a technology based on the Genomewide Ligation of 3’-OH Ends (GLOE-Seq) and an associated computational pipeline designed for single-stranded breaks (SSBs), but versatile enough to be applied to any lesion that is convertible into a free 3’-OH terminus. We demonstrate its applicability to the mapping of Okazaki fragments without prior size selection and detect biases and asymmetries in the distribution of spontaneous SSBs in budding yeast and human DNA.

2020-04-21 | GSE134219 | GEO

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [Human_Ligase_inactivation]

2020-04-21 | GSE134224 | GEO

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [UV treatment]

2020-04-21 | GSE134222 | GEO

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [HO endonuclease]

2020-04-21 | GSE134221 | GEO

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [MMS treatment]

2020-04-21 | GSE145032 | GEO

Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [CDC9 inactivation]

2020-04-21 | GSE134223 | GEO