Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

ABSTRACT: Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

PROVIDER: PRJNA1132236 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

Project description:Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

| PRJNA1132231 | ENA

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (4)

Project description:To explore the expression of eccDNA in patients with liver cirrhosis and liver cancer, focusing on their impact on disease development.

2025-01-29 | GSE271574 | GEO

Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer (2)

Project description:To explore the expression of eccDNA in patients with chronic hepatitis B and liver cirrhosis, focusing on their impact on disease development.

2025-01-29 | GSE271570 | GEO

Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

Project description:Extrachromosomal circular DNAs (eccDNAs) have been discovered in various species and play a significant role in cancer development However, our understanding of eccDNAs in normal cells is limited. Here, we conducted eccDNA sequencing by Circle-seq in undifferentiated human bone marrow mesenchymal stem cells (uhBMSCs) and their differentiation into osteoblasts (OBs), chondrocytes (CCs), and adipocytes (ACs) to gain knowledge about eccDNAs in cell differentiation,

2025-01-31 | GSE261856 | GEO

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

eccDNA in maternal plasma

Project description:We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.

| EGAS00001003827 | EGA

Whole-genome sequencing of Extrachromosomal circular DNA (eccDNA) of cerebrospinal fluid of Medulloblastoma

Project description:Background: Medulloblastoma (MB) is one of the malignant tumors of the central nervous system (CNS) with a poor prognosis and lack of effective detection. Extrachromosomal circular DNA (eccDNA) has been reported to be closely related to CNS tumors. However, there is still a gap in eccDNA of MB.Methods: Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) using a circle-map, compared with normal. The nucleotides on both sides of the eccDNAs breakpoint were analyzed to investigate the mechanisms of eccDNAs formation. Bioinformatics analysis combined with the GEO database identified reliable features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan–Meier curve were used to assess the potential diagnostic and prognostic value of the Hub genes.Results: 35179 eccDNAs were identified, with the majority less than 1000 base pairs (bp). The distribution of eccDNAs on the genome was closely related to gene density. EccDNAs in CSF exhibited phase parallelism with matched MB tissues and were shown differently in tumors and normal. Ten core genes were identified in combination with GEO and showed reliable diagnostic and prognostic value in independent datasets through univariate and multivariate Cox regression. Nomogram included Hub-gene signatures was established and showed clinical benefit.Conclusions: This study described the characteristics and formation mechanism of eccDNAs in MB and CSF. The role of eccDNA in MB was revealed, and eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.

2022-10-20 | GSE205178 | GEO

Serum microRNA expression in patients with HBV-related liver cirrhosis and bacterial infection.

Project description:Hepatitis B virus-related liver cirrhosis (HBV-LC) is susceptible to bacterial infections, which could lead to adverse prognosis in patients. MicroRNA (miRNA) is easily detected in peripheral blood and is involved in multiple liver diseases. This pilot study aimed to investigate the differentially expressed (DE) miRNAs in the serum of patients with HBV-LC and bacterial infection, and to identify the potential biomarker. The clinical samples was collected, including four patients with HBV-LC and infection, four patients with HBV-LC without infection, four patients with chronic hepatitis B (CHB) and four healthy controls. miRNA expression was analyzed by Affymetrix GeneChip miRNA 4.0 Array. A total of 385 DE miRNAs (upregulated, 160; downregulated, 225) were detected in patients with HBV-LC and infection compared with patients with HBV-LC without infection.

2020-08-18 | GSE156347 | GEO

Huh-7 exosomes and HBV

Project description:Hepatitis B virus (HBV) infection could cause hepatitis, liver cirrhosis and hepatocellular carcinoma. HBV-mediated pathogenesis is only partially understood, but X protein (HBx) reportedly possesses oncogenic potential. Exosomes are small membrane vesicles with diverse functions released by various cells including hepatocytes, and HBV harnesses cellular exosome biogenesis and export machineries for virion morphogenesis and secretion. Therefore, HBV infection might cause changes in exosome contents with functional implications for both virus and host. In this project, exosome protein content changes induced by HBV and HBx were quantitatively analyzed by SILAC/LC-MS/MS. Exosomes prepared from SILAC-labeled hepatoma cell line Huh-7 transfected with HBx, wildtype or HBx-null HBV replicon plasmids were analyzed by LC-MS/MS.

2017-03-29 | MSV000080794 | MassIVE

CIRCLE-seq analyais for -175 site

Project description:Adenosine base editing to recreate the HPFH mutations is a promising approach to induce HbF. We used CIRCLE-seq to identify 682 potential off-target sites in purified DNA treated with Cas9 nuclease complexed to sgRNA targeting -globin -175 .

2023-04-28 | GSE228569 | 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