GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL18573

96 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

48 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

2 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

12 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

4 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

22 Samples

Download data: BW

(Submitter supplied) We have designed a methodology for capture of DNA 3’ ends that allows mapping of resected DNA breaks, stalled replication forks and also normal replication fork progression. This Transferase-activated end ligation or TrAEL-seq method involves ligation of a functionalised linker to DNA 3’ ends followed by fragmentation, purification of adaptor ligated fragments, second adaptor ligation and library amplification. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL19756 GPL17143

46 Samples

Download data: TXT

(Submitter supplied) We show that ligation-competent Okazaki fragments in Saccharomyces cerevisiae are sized according to the chromatin repeat. Using deep sequencing, we demonstrate that ligation junctions preferentially occur around nucleosome midpoints rather than in internucleosomal linker regions. Disrupting chromatin assembly or lagging strand polymerase processivity impacts both the size and the distribution of Okazaki fragments, suggesting a role for nascent chromatin, assembled immediately after the passage of the replication fork, in the termination of lagging strand synthesis. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

4 Samples

Download data: BED

(Submitter supplied) Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, the nonrandom distribution of meiotic DSBs along the genome can be attributed to the combined influence of multiple factors on Spo11 cleavage. One factor is higher-order chromatin structure, particularly the loop-axis organization of meiotic chromosomes. Axial element proteins Red1 and Hop1 provide the basis for meiotic loop-axis organization and are implicated in diverse aspects of meiotic recombination. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

6 Samples

Download data: WIG

(Submitter supplied) 8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Several thousand residues of 8-oxodG spread constitutively in the genome of human cells, but their genomic distribution has not yet been characterized. Here, by using OxyDIP-Seq, a highly sensitive methodology that uses high-throughput sequencing, we report the first genome-wide distribution of 8-oxodG in human cells, using the non-tumorigenic epithelial breast cells MFC10A. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

8 Samples

Download data: BED

(Submitter supplied) We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA. We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast Keywords: dose

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS2508

Platform:

GPL90

18 Samples

Download data

Analysis of cells exposed to the radiomimetic enediyne antibiotics calicheamicin, esperamicin A1, and neocarzinostatin. These enediynes bind specifically to DNA and generate single- and double-strand DNA breaks. Results provide insight into the response to DNA damage.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 6 agent sets

Platform:

GPL90

Series:

GSE5301

18 Samples

Download data

(Submitter supplied) Prior to ligation, each Okazaki fragment synthesized on the lagging strand in eukaryotes must be nucleolytically processed. Nuclease cleavage takes place in the context of 5’ flap structures generated via strand-displacement synthesis by DNA polymerase delta. At least three DNA nucleases: Rad27 (Fen1), Dna2, and Exo1, have been implicated in processing Okazaki fragment flaps. However, neither the contributions of individual nucleases to lagging-strand synthesis nor the structure of the DNA intermediates formed in their absence have been clearly defined in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

16 Samples

Download data: BEDPE

(Submitter supplied) We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL9377

1 Sample

Download data: BED

(Submitter supplied) Multiple DNA polymerases are needed to replicate genetic information. Here we describe the use of ribonucleotide incorporation as a biomarker of replication enzymology in vivo. We find that ribonucleotides are incorporated into the yeast nuclear genome in replicase specific and strand-specific patterns that identify replication origins and where polymerase switching occurs. Ribonucleotide density varies across the genome as a function of the replicase, base, local sequence and proximity to nucleosomes and transcription start sites. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

29 Samples

Download data: BEDGRAPH, FA, GFF3

(Submitter supplied) The Saccharomyces cerevisae RAD3 gene is homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Mutant alleles of RAD3 have been identified (rad3-101 and rad3-102) that have partial defects in DNA repair associated with a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platforms:

GPL21274 GPL20143

96 Samples

Download data: GPR, XLSX

(Submitter supplied) We developed a method for genome-wide mapping of DNA excision repair named XR-seq (eXcision Repair-seq). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a ~30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells, cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts ((6-4)PPs). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

12 Samples

Download data: BW

(Submitter supplied) Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. Herein, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL21273 GPL20795

109 Samples

Download data: BED

(Submitter supplied) Platinum chemotherapies induce damages in DNA that distort the helical structure. In human cells, these adducts are removed primarily by the Nucleotide Excision Repair pathway. In this study, we mapped both cisplatin and oxaliplatin induced damages and their repair at single nucleotide resolution across the human genome.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

14 Samples

Download data: BW