GEO DataSets

(Submitter supplied) The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL15520 GPL10999

5 Samples

Download data: TXT

(Submitter supplied) Nucleic acid secondary structures play a critical role in the regulation of biological processes. Genome-wide detection of DNA and RNA secondary structures is essential to identify pathways that are regulated by nucleic acid folding. There are no methods to interrogate DNA secondary structure formation on a genome-wide scale. We present G4-Seq, a method that applies the concept of polymerase interference at G-quadruplex (G4) DNA secondary structures to a human genome scale by massively parallel array-sequencing. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: BED, BEDGRAPH, TDF, TXT

(Submitter supplied) G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. Herein we address this through the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18573

52 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) G-quadruplex (G4) structure is an alternative conformation of the double helical structure of B-form DNA arisen in guanine-rich sequences . The formation of G4 structures can influence chromatin architecture and many fundamental biology processes, such as DNA replication and gene regulation . We present G4-miner, a genome-wide approach to directly identify G4 structures from ordinary sequencing data. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

2 Samples

Download data: BED

(Submitter supplied) 8-Oxo-7,8-dihydro-2’-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

10 Samples

Download data: BW

(Submitter supplied) We report the RNA-seq data for rat nucleus pulposus cells after stabilizing G-Quadruplexes (G4). We sequenced rat nucleus pulposus cells treated with PDS, Braco-19 and Phen-DC3 separately and untreated with these G4 stabilizers, which could stabilize G4 structure in cells.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

18 Samples

Download data: TXT