Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6294800.fastq.gz | Fastqsanger.gz | |||
| SRR6294810.fastq.gz | Fastqsanger.gz | |||
| SRR6294801.fastq.gz | Fastqsanger.gz | |||
| SRR6294811.fastq.gz | Fastqsanger.gz | |||
| SRR6294802.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:We performed all stimulatory experiments using THP1 cell line as a representative of primary human monocytes to show fundamental role of the cfDNA in healthy organisms. The experiments were conducted in duplicates using plasma containing cfDNA (NP) and the reference one with cfDNA removed by DNase (TP) to recognize unequivocally the effect of plasma cfDNA on transcriptome and proteome of monocytes. We used native human plasma samples obtained from healthy volunteers with no animal serum addition to cultivation medium in order to avoid the presence of uncharacterized animal cfDNA in the experiments.
2021-05-18 | PXD017285 | Pride
Project description:Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible. Sequencing of cfDNA libraries from healthy individuals, pooled healthy individuals and individuals with disease for the identification of nucleosomes and protection from other DNA binding proteins.
2015-11-04 | E-GEOD-71378 | biostudies-arrayexpress
Project description:The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method can identify pregnant women with AID during routine non-invasive prenatal screening. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.
2022-09-14 | E-MTAB-11607 | biostudies-arrayexpress
Project description:Circulating cfDNA based Low-pass WGBS in hepatocellular carcinoma surveillance
| PRJNA564401 | ENA
Project description:Increased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with acute cellular rejection (ACR) after heart transplantation. DNA sequence differences have been used to distinguish between donor and recipient cfDNA but epigenetic differences could also potentially identify dd-cfDNA. This study aimed to assess the feasibility of using ventricle-specific methylation patterns in human cfDNA as an alternative biomarker for ACR in cardiac transplantation.
2020-06-18 | GSE152648 | GEO
Project description:The epigenome of plasma cell-free DNA (cfDNA) has demonstrated promise as both a prognostic and predictive cancer biomarker in liquid biopsies. Currently, it remains unknown whether and why cfDNA 5-hydroxymethylcytosine (5hmC) can identify disease state for non-small cell lung cancer (NSCLC). We profiled 5-hydroxymethylomes using the plasma cfDNA of 302 EGFR-mutant NSCLC patients with different disease states. We found NSCLCs were epigenetically heterogeneous among individuals, especially for cfDNA 5hmC on gene EGFR. The diversity of age, sex, race, smoking status, EGFR-mutation of patients increased the epigenetic heterogeneity of NSCLC, however, only smoking status shaped disease state-associated cfDNA 5hmC. More importantly, disease state-dependent and patients’ characteristics-independent cfDNA 5hmC can be linked to lung function and regulatory elements in human lung cells. Interestingly, although 5-hydroxymethylome heterogeneity of plasma cfDNA among NSCLC patients were detected substantially, cfDNA-5hmC-based machine learning model can accurately predict different disease state in NSCLC.
2025-01-29 | GSE231296 | GEO
Project description:Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible.
2015-11-04 | GSE71378 | GEO
Project description:Molecular biomarkers to monitor changes after liver transplant are essential to reveal mechanisms of injury, guide clinical decision-making and improve patient outcomes. Current approaches have limited scope and are unable to differentiate between host and graft amongst the causes of graft injury. Here, we utilize circulating, cell-free methylated DNA released from dying cells to monitor cellular damages after liver transplant impacting the graft tissue as well as host organs. We expand existing cell-type-specific DNA methylation atlases curated from whole-genome bisulfite sequencing (WGBS) of healthy tissues to characterize liver cell-types relevant to injury progression and tissue repair. Liver cell-type-specific methylation blocks are validated through multi-omic data integration and found to be enriched in open chromatin and regulatory regions functionally important for the respective cell populations. Cell-free DNA (cfDNA) fragments were captured from patient serum by hybridization to CpG-rich DNA panels and mapped to the expanded DNA methylation atlases to inform tissue origins of cell types. We profiled 135 blood samples collected from 44 liver transplant patients at serial time points before and after transplant. We found that liver transplant initially results in multi-tissue cellular damage that subsequently recovers in patients with graft acceptance during the first post-operative week. Further, we show that sustained elevation of hepatocyte and biliary epithelial cfDNA beyond the first week is indicative of early-onset graft injury. Most notably, cfDNA composition can differentiate amongst causes of graft injury. Thus, cell-free methylated DNA can detect cellular damages and prompt early intervention.
2025-03-02 | GSE263243 | GEO