Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ecc_finder: a robust and accurate tool for detecting extrachromosomal circular DNA from sequencing data

ABSTRACT: Ecc_finder is a comprehensive tool to detect extrachromosomal circular DNA from short and long read sequencing

PROVIDER: PRJEB46420 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR6326000_1.fastq.gz	Fastqsanger.gz
	ERR6326000_2.fastq.gz	Fastqsanger.gz
	ERR6326020.fastq.gz	Fastqsanger.gz
	ERR6326021.fastq.gz	Fastqsanger.gz
	ERR6326084_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data.

Project description:Extrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this specific type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there are several protocols for enriching eccDNAs and performing short-read or long-read sequencing. However, there is currently no available bioinformatic tool to identify eccDNAs from Nanopore reads. More importantly, the current tools based on Illumina short reads lack an efficient standardized pipeline notably to identify eccDNA originating from repeated loci and cannot be applied to very large genomes. Here, we introduce a comprehensive tool to solve both of these two issues. Applying ecc_finder to eccDNA-seq data (either mobilome-seq, Circle-Seq and CIDER-seq) from Arabidopsis, human, and wheat (with genome sizes ranging from 120Mb to 17 Gb), we document the improvement of computational time, sensitivity, and accuracy and demonstrate ecc_finder wide applicability and functionality.

| S-EPMC8672306 | biostudies-literature

Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [eccDNA-seq]

Project description:Extrachromosomal circular DNA (eccDNA) is double-stranded circular DNA that is derived from but independent of chromosomal DNA. Owing to its nonchromosomal inheritance, eccDNA facilitates the amplification of oncogenes and expedites the process of genome evolution in tumor. However, the role of eccDNA in RB remains enigmatic. We combined Circle-Seq and RNA-Seq to identified crucial extrachromosomal circular oncogene amplicons. Herein, we revealed that extrachromosomal circular SUZ12 amplicon regulates H3K27me3 modification during the oncogenic progression of retinoblastoma. Conclusively, our study initially delineated an integrated picture of the eccDNA landscape in retinoblastoma and unveiled a novel SUZ12-containing eccDNA/H3K27me3 oncogenic mechanism where eccDNA dictates retinoblastoma progression through regulating transcription levels of linear DNA.

2023-07-02 | GSE235888 | GEO

Effects of nucleases on cell-free extrachromosomal circular DNA

Project description:Effects of nucleases on cell-free extrachromosomal circular DNA

| EGAS00001005873 | EGA

Characteristics of circular extrachromosomal DNA in euglenids

Project description:Characteristics of circular extrachromosomal DNA in euglenids

| PRJEB67978 | ENA

Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

Project description:Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

| PRJNA1100545 | ENA

Genome-scale purification of extrachromosomal circular DNA in yeast.

Project description:Extrachromosomal circular DNA is common in yeast.

| PRJEB6368 | ENA

ATAC-seq identifies thousands of extrachromosomal circular DNA in cancers and cell lines

Project description:Extrachromosomal circular DNAs (eccDNAs) are usually somatically mosaic and a source of intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments, without any enrichment of circular DNA, and thus identified thousands of eccDNAs. The eccDNAs identified in cell lines were validated by inverse PCR on DNA that survives exonuclease digestion of linear DNA, and by metaphase FISH. ATAC-seq in Gliomas and Glioblastomas identify hundreds of eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. Over 18,000 eccDNAs, many carrying known cancer driver genes, are identified in a pan-cancer analysis of 360 ATAC-seq libraries from 23 tumor types. Because of somatic mosaicism, eccDNAs are identified by ATAC-seq even before amplification of the locus is recognized by genome-wide copy number variation measurements. Thus, standard ATAC-seq is a sensitive method to detect eccDNA present in a subset of tumor cells, ready to be amplified under appropriate selection, as during therapy.

2020-02-18 | GSE145409 | GEO

The Adaptational Dynamics of Extrachromosomal Circular DNA in Rice

Project description:The Adaptational Dynamics of Extrachromosomal Circular DNA in Rice

| PRJEB59090 | ENA

Characterization of extrachromosomal circular DNA for human dilated cardiomyopathy

Project description:Characterization of extrachromosomal circular DNA for human dilated cardiomyopathy

| PRJNA1008715 | ENA

Circular extrachromosomal DNA drives massive oncogene expression and chromatin accessibility

Project description:Oncogenes are commonly amplified on extrachromosomal DNA particles (ecDNA) in cancer, but our understanding of the structure of ecDNA and its impact on gene regulation is limited. We integrated ultrastructural imaging, long range-optical mapping, and computational analysis of whole genome sequencing to demonstrate unequivocally that ecDNA is circular. Pan-cancer analyses reveal that the oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of tumours, linking elevated copy with very high levels of transcription. Quantitative assessment of the chromatin state, including ATAC-seq to map the accessible genome and ATAC-see to examine spatial distribution of open chromatin, reveal that while ecDNA is chromatinized, it lacks higher order compaction typical of chromosomes. In fact, ecDNA contains the most accessible DNA in the tumour genome. Using chromosome conformation capture technologies and CRISPR interference, we reveal the differential organization of active chromatin in cancer that is dictated by the circular shape of ecDNA. Lastly, we develop comprehensive maps that provide new insight into how circular ecDNA structure determines oncogene function, bridging ecDNA biology with modern cancer genomics and epigenetics.

2019-12-31 | GSE131956 | GEO

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