Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

ABSTRACT: Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

PROVIDER: PRJNA836112 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19135478_1.fastq.gz	Fastqsanger.gz
	SRR19135478_2.fastq.gz	Fastqsanger.gz
	SRR19135479_1.fastq.gz	Fastqsanger.gz
	SRR19135479_2.fastq.gz	Fastqsanger.gz
	SRR19135480_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Single-stranded Pre-methylated 5mC Adapters Uncover the Methylation Profile of Plasma Ultrashort Single-stranded Cell-free DNA

Project description:Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ~50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the “5mCAdpBS-Seq” workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (~15%) and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment positively affected gene expression of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.

2024-03-28 | GSE252088 | GEO

Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

Project description:We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC). Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).

2022-05-10 | GSE202430 | GEO

Effect of Oral Administration of Methylene Blue MMX Tablets on Double Stranded DNA

Project description:Single Centre, open label assignment phase II clinical study. To evaluate the effect of oral 200mg Methylene Blue tablets (administered 8x25mg) prior to endoscopy on double stranded DNA breaks in colonic biopsy samples assessed by histone gamma H2AX analysis, compared to control biopsies.

| 2178654 | ecrin-mdr-crc

single-stranded DNA study

Project description:A ssDNA library protocol was applied to cfDNA from plasma samples obtained from different DNA extraction methods and revealed significant differences in DNA fragmentation patterns in comparison to dsDNA-based protocols. In particular, a specific combination of methods revealed a population of ultrashort fragments, organized at ~50 bp. We observed significant differences in the relative abundance of these ultrashort DNA fragments in plasma from healthy individuals and cancer patients. Through shallow whole genome sequencing (sWGS, <0.5-fold coverage) and the analysis of somatic copy number aberrations (SCNA), we determined the landscape of genetic alterations in this newly identified population of cfDNA fragments. In addition, we studied their potential link with regulatory regions by investigating the genome-wide coverage patterns at transcription start sites (TSS). Furthermore, we demonstrated that the ultrashort cfDNA fragments map to regions associated with secondary DNA structures, G-quadruplexes (G4s).

| EGAS00001005093 | EGA

Project description:Single-stranded Premethylated 5mC Adapters Uncovers the Methylation Profile of Plasma Ultrashort Single-Stranded Cell-Free DNA

| PRJNA980280 | ENA

DNA methylation analysis of the cell free DNA from Retinoblastoma

Project description:DNA methylation analysis of the cell free DNA from Retinoblastoma

| PRJNA804516 | ENA

Circulation cell-free DNA as a biomarker applied in clinical practice of gastrointestinal tumor

Project description:Interventions: Gold Standard:;Index test: Primary outcome(s): concentration of cell-free DNA in plasma;integrity of cell-free DNA in plasma Study Design: Diagnostic test: case-control

| 2662278 | ecrin-mdr-crc

Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes

Project description:Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes

| PRJNA630205 | ENA

Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

Project description:Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

| PRJNA1090946 | ENA

Project description:Distinct Features of Plasma Ultrashort Single-Stranded Cell-Free DNA as Biomarkers for Lung Cancer Detection

| PRJNA978642 | ENA