Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Composition and structure of Arabidopsis thaliana extrachromosomal circular DNAs revealed by nanopore sequencing

PROVIDER: PRJNA975338 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24693334_1.fastq.gz	Fastqsanger.gz
	SRR24693335_1.fastq.gz	Fastqsanger.gz
	SRR24693336_1.fastq.gz	Fastqsanger.gz
	SRR24693337_1.fastq.gz	Fastqsanger.gz
	SRR24693338_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Project description:Extrachromosomal circular DNA in Arabidopsis thaliana

| PRJNA572559 | ENA

Project description:Extrachromosomal circular DNA in Arabidopsis thaliana

| PRJNA497665 | ENA

Engineered extrachromosomal circular DNAs promote tumorigenesis (WGS)

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

| PRJNA1100545 | ENA

Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

Project description:Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

2022-08-06 | E-MTAB-12009 | biostudies-arrayexpress

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues

Project description:We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200-400 bp long, derived from unique non-repetitive sequence and are enriched in the 5' untranslated regions of genes, exons and CpG islands. Chromosomal loci that are enriched sources of microDNA in adult brain are somatically mosaic for micro-deletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a new DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci. Circular DNA profiling by high throughput sequencing

2012-02-27 | E-GEOD-36088 | biostudies-arrayexpress

Project description:Arabidopsis thaliana and Heterodera schachtii total circular DNAs libraries using Illumina-seq

| PRJNA1020889 | ENA

Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

2022-11-07 | GSE211295 | GEO

Long-read cDNA Sequencing of Transposable Element-Activated Arabidopsis Mutants

Project description:We have used the genetic resources of Arabidopsis thaliana to generate mutant lines that have reactivated TE expression. We used these lines with long-read Oxford Nanopore sequencing technology to capture Transposable Element (TE) mRNAs for TE transcript annotation.

2020-07-17 | GSE145066 | GEO

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells

Project description:Oncogenic extrachromosomal DNAs (ecDNA) are common in cancers, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe scEC&T-seq, a method for parallel isolation and sequencing of extrachromosomal circular DNAs and full-length mRNA from single human cells. By applying scEC&T-seq to cancer cells, we not only describe intercellular differences in ecDNA content, but also investigate their structural heterogeneity and transcriptional impact. We reveal that whereas oncogene-containing ecDNA elements are clonally present in cancer cells and drive intercellular oncogene expression differences, other small circular DNAs also captured by scEC&T-seq are mostly private to individual cancer cells, indicating differences in selection and propagation. Moreover, scEC&T-seq uncovers intercellular differences in ecDNA structure, which allowed the inference of ecDNA structural dynamics and point to circular recombination as a potential mechanism of ecDNA evolution. We envision that our method may enable the analysis of yet unknown prerequisites for the maintenance of both small and large circular DNA in cancers, but also in the context of other diseases and normal cellular development.

| EGAS00001007026 | EGA

Generation of full-length circRNA libraries for Oxford Nanopore long-read sequencing

Project description:Preparation of libraries for circular RNA sequencing with Oxford Nanopore long-read sequencing

2022-08-09 | GSE197872 | GEO