Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RRBS-seq of single-cell clones of four cell Lines reveals highly-conserved methylated sites in DNA

ABSTRACT: DNA methylation is one of the most studied epigenetics, and its effects on embryonic development, cell differentiation, cell development, aging, apoptosis, carcinogenesis, and genomic stability are all im-portant. In the classical epigenetic model, cytosine methylation is steadily transmitted to daughter cells with fidelity as DNA replicates. However, a large number of studies have shown that there are detectable changes in DNA methylation at many CpG sites during DNA replication. In this study, we selected four different types of cell lines, A549, ARPE-19, Jurkat and SW1353. For a single CpG site in a single cell, there are only three methylation states, 100% methylation, 50% methylation, and 0% methylation, and any DNA methylation that deviates from these three results indicates a methylation change. We used reduced representative bisulfite sequencing (RRBS) to screen out methylation sites.

ORGANISM(S): Homo sapiens

PROVIDER: GSE308367 | GEO | 2025/09/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RRBS-seq of single-cell clones of four cell Lines reveals highly-conserved methylated sites in DNA [RNA-Seq]

Project description:DNA methylation is one of the most studied epigenetics, and its effects on embryonic development, cell differentiation, cell development, aging, apoptosis, carcinogenesis, and genomic stability are all im-portant. In the classical epigenetic model, cytosine methylation is steadily transmitted to daughter cells with fidelity as DNA replicates. However, a large number of studies have shown that there are detectable changes in DNA methylation at many CpG sites during DNA replication. In this study, we selected four different types of cell lines, A549, ARPE-19, Jurkat and SW1353. For a single CpG site in a single cell, there are only three methylation states, 100% methylation, 50% methylation, and 0% methylation, and any DNA methylation that deviates from these three results indicates a methylation change. We used reduced representative bisulfite sequencing (RRBS) to screen out methylation sites.

2025-09-19 | GSE308366 | GEO

RRBS-based quantitative methylation analysis define 100% methylation fidelity CpG sites

Project description:Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. This study introduced a RRBS-based quantitative method to identify CpG sites of high methylation fidelity (especially those 100% methylation fidelity sites). To separate the 100% methylation fidelity sites , we cultured the ARPE-19, Jurkat and SW1353 cells for lasting 10 generations, and we detected the methylation level of each CpG sites in the 20th generation and the 30th generation by performing reduced representation bisulfite sequencing (RRBS), to obtain the 100% methylation fidelity sites. The result shows that the number of overlapped fidelity methylation CpG sites of the two different time is smaller than number of each generation. Our results also showed that the proportion of high-fidelity 100% methylated sites in Jurkat and ARPE-19 cells is about 4.4% and 8.9%, and the proportion in SW1353 cells is 1.98%. The fidelity methylation sites obtained by the comparison of the two different time periods are the truly unchanged CpG sites during cell passage, which improves the reliability of the fidelity methylation sites. In summary, we provide new insights into the DNA methylation fidelity study.

2021-06-08 | GSE176335 | GEO

Detection of Colorectal Cancer in Peripheral Blood by Septin 9 DNA Methylation Assay

Project description:Epigenomics is developing a colon cancer screening assay based on differential methylation of specific CpG sites for the detection of early stage disease. A genome-wide methylation analysis and oligonucleotide array study using DNA from various stages of colon cancer and normal tissue have been completed to obtain candidate CpG markers. Based on results obtained in the above studies, Epigenomics has moved to the final stages of feasibility with a specific, highly sensitive real-time marker assay that is able to detect colon cancer DNA in blood plasma.

| 2056787 | ecrin-mdr-crc

The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [MNase-seq]

Project description:Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. To investigate the relationship of stably high methylation sites with gene expression, we cultured the ARPE-19 for lasting 10 generations and performed reduced representation bisulfite sequencing (RRBS) to obtain the highly methylated sites. Then we analyzed the characters of highly methylated sites and detected the transcription level of the cells. After filtered the low methylated CpG island (CGI), we found that highly methylated CpG sites had a preference for CGI boundary. In the promoter CGI, only in the condition as the gene expression is inhibited and the promoter CGI is at a high methylation level, a significant enrichment of the highly methylated sites is observed in the promoter CGI boundary. Our results showed that the enrichment of high methylation sites at the boundary of the CGI in the promoter region would have a significant inhibitory effect on the gene expression. In summary, we provide new insights into the regulatory mechanisms of DNA methylation.

2021-06-08 | GSE176336 | GEO

The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [RNA-seq]

2021-06-07 | GSE176234 | GEO

Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome

Project description:DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We find that the percentage of unmethylated CpGs is relatively fixed regardless of cell type. However, which CpGs are unmethylated is cell-type specific. We categorize the 26 million human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs. Among all the autosomal CpGs, 22.6% exhibit variable DNA methylation across cell types included in our study. These variably methylated CpGs form 66 thousand variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enrich for transcription factor binding sites in a tissue-dependent manner. Importantly, they enrich for GWAS variants, suggesting VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link among CpG methylation variation, genetic variation and disease risk in a tissue-specific manner for many human cell types. Processed data includes new Samples and 75 Samples from GSE16368 and 2 Samples from GSE51565.

2016-04-06 | E-GEOD-69894 | biostudies-arrayexpress

Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome

2016-04-06 | GSE69894 | GEO

Correlation Between SFRP1 and Colorectal Cancer and Adenoma

Project description:In summary, our study demonstrated the methylation sites of SFRP1 gene promoter in patients with colorectal cancer and adenoma and found SFRP1_16_17_18 CpG site was good performance as a diagnostic marker of colorectal cancer.

| 2401959 | ecrin-mdr-crc

DNA Methylation Changes in Whole Blood and CD16+ Neutrophils in Response to Chronic Folic Acid Supplementation in Women of Childbearing Age

Project description:Folate, a water-soluble vitamin, is a key source of one-carbon groups for DNA methylation, but studies of the DNA methylation response to supplemental folic acid yield inconsistent results. The aim of this study was to determine if DNA methylation patterns in the dominant white blood cell type, neutrophils, would respond differently than whole blood in response to chronic folic acid supplementation. Saliva and blood methylation was clearly distinguishable though there was positive correlation overall. There was little correlation in CpG sites within relevant candidate genes. Correlated CpG sites were more likely to occur in areas of low CpG density (i.e. CpG shores and open seas). There was more variability in CpG sites from saliva than blood, which may reflect its heterogeneity. Thus, this study provides a framework for using DNA methylation from saliva and suggests that DNA methylation of saliva may offer distinct opportunities for epidemiological and longitudinal studies of psychiatric traits.

2014-11-21 | GSE63499 | GEO

PIAMA DNA methylation dataset

Project description:Nasal DNA methylation at three CpG sites predicts childhood allergic disease

| EGAD00010002263 | EGA