Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma

ABSTRACT: The genome-wide analysis of cfDNA fragmentation patterns in DENQCMs and maternal plasma was performed by deep sequencing using Illumina Novaseq to confirm their biological characteristics. We first performed deep whole genome sequencing of the cfDNA extracted from DENQCMs and maternal plasma cfDNA. Then we analyzed the sequencing data and compared various characteristics of cfDNA fragmentation patterns, such as dinucleotide composition, nucleosome protection length, and nucleosome occupancy based on a windowed protection score (WPS), to the submitter-provided processed data from a healthy individual IH01 (GEO accession GSM1833276).

ORGANISM(S): Homo sapiens

PROVIDER: GSE124686 | GEO | 2019/01/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma

Project description:Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma

| PRJNA513060 | ENA

Exposure of THP1 cells to plasma containing or lacking cfDNA

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

Exposure of THP1 cells to plasma containing or lacking cfDNA

Project description:We aimed to clarify the cell-free DNA (cfDNA) physiological role. We exposed THP1 cells to plasma from healthy individuals with and without cfDNA and compared their transcriptomes and proteomes.

2020-12-01 | E-MTAB-8574 | biostudies-arrayexpress

Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin

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

Nucleosome footprinting in plasma cell-free DNA for diagnosis of ovarian cancer

Project description:Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals.

| EGAS00001005361 | EGA

Sequencing of cfDNA derived from the plasma of individuals of different ages

Project description:We provide the first in vivo evidence of global and local chromatin changes in human aging by analyzing cfDNA from the blood of individuals of different age groups. Our results show that nucleosome signals inferred from cfDNA are consistent with the redistribution of heterochromatin observed in cellular senescence and aging in other model systems. It also revealed age and deteriorating health status correlate with a low-level enrichment of signals from cells in the thyroid gland. In addition, we detected an overall nucleosome loss at several genomic locations, such as transcription start and termination sites, 5’UTR of L1HS retrotransposons and dimeric AluY elements with age.

2018-12-21 | GSE114511 | GEO

Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin

2015-11-04 | GSE71378 | GEO

Genome-wide DNA methylation analysis in cfDNA from pancreatic cancer patients

Project description:Heterogeneity in DNA methylation status may exist between primary tumors and cfDNA. We compared the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients. MBD-sequencing (seq) was performed in paired samples of FNA and cfDNA from two patients. The majority of DNA methylation peaks overlapped in FNA and cfDNA samples (82.6% and 82.9% in patients #1 and #73, respectively). DNA methylation levels of each gene in FNA and cfDNA samples were highly correlated with each other (r=0.98 and 0.97 in samples 1 and 73, respectively)

2020-05-21 | GSE150468 | GEO

cfDNA sequencing with TACS-TOPO scheme

Project description:Human cfDNA was extracted from human serum, and served for sequencing library preparation with TACS-TOPO scheme.

2023-08-30 | GSE222918 | GEO

Longitudinal analysis of personal cfDNA methylome patterns in metastatic prostate cancer [plasma]

Project description:Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our study aimed to investigate the dynamics of personal methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. 52 plasma samples from 9 patients with mPCa were collected, longitudinally, over 13-21 months. After cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip and analysed using the minfi software. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify and validate ctDNA differentially methylated genes (DMGs). Personal cfDNA global methylation patterns were temporally stable throughout disease course. A proportion of analysed CpG sites presented a dynamic temporal pattern that was consistent with clinical events, such as therapy administration, and were prominently associated with immune response pathways. Study of ctDNA identified >2,000 DMGs with dynamic methylation patterns. We concluded that longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with the occurrence of specific clinical events, thus highlighting the potential of using liquid biopsies to study PCa progression.

2021-09-01 | GSE157273 | 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