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ProteomicsExposure of THP1 cells to plasma containing or lacking cfDNA
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 (...
ORGANISM(S): Homo sapiens (Human) 
2021-05-18 | PXD017285 | Pride
Thp1 cells Plasma Cfdna 
TranscriptomicsGenome-wide plasma cell-free DNA methylation profiling in lung cancer patients using MeDIP-seq
As a non-invasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma is raising increasing interest due to its diagnostic and biology applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. Through enriching methyla...
ORGANISM(S): Homo sapiens 
2019-03-31 | E-MTAB-7163 | biostudies-arrayexpress
TranscriptomicsEpigenome analysis of cfDNA samples from lung cancer patients and tumor free individuals with respiratory diseases
There is a growing recognition of the importance of conducting epigenome-wide analysis directly in cfDNA to identify specific, blood-measurable DNA methylation biomarkers. In this study, we ought to identify novel epigenetic biomarkers for lung cancer (LC) detection from blood-derived cfDNA. Using t...
ORGANISM(S): Homo sapiens 
2026-09-01 | E-MTAB-15459 | biostudies-arrayexpress
ProteomicsPre-Analytical Framework for Routine Clinical Use of Liquid Biopsies: Combining EVs and cfDNA
Liquid biopsies hold significant potential for the non-invasive diagnostics of tumors and other diseases. While the clinical application of cell-free DNA (cfDNA) methodologies is emerging, the implementation of tumor-derived extracellular vesicles (EVs) as validated biomarkers is hindered by substan...
ORGANISM(S): Homo sapiens (Human) 
2026-01-23 | PXD062837 | Pride
Extracellular vesicles Liquid biopsy Cfdna Human plasma Tube preservation Isolation protocol Pre-analytics Translation 
TranscriptomicsExposure of THP1 cells to plasma containing or lacking cfDNA
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.
ORGANISM(S): Homo sapiens 
2020-12-01 | E-MTAB-8574 | biostudies-arrayexpress
GenomicscfDNA sequencing with TACS-TOPO scheme
cfDNA sequencing with TACS-TOPO scheme
PRJNA924027 | ENA
GenomicsIntegrative Whole-Genome and Epigenome profiling of cfDNA in Familial Prostate Cancer: Insights from a Pilot Study
Prostate cancer (PCa) is one of the most common malignancies in men, with familial forms accounting for nearly 20% of cases. Early detection and risk stratification remain challenging, especially in individuals with a genetic predisposition. In this pilot study, we evaluated the feasibility and clin...
ORGANISM(S): Homo sapiens 
2026-06-15 | E-MTAB-15437 | biostudies-arrayexpress
GenomicscfDNA methylation data of longitudinally collected blood plasma samples from patients with esophageal adenocarcinoma
This study aimed to evaluate the cost-effective and genome-wide cell-free reduced representation bisulfite sequencing (cfRRBS) method combined with computational deconvolution for effective disease monitoring in patients with esophageal adenocarcinoma (EAC). cfDNA methylation profiling with cfRRBS w...
ORGANISM(S): Homo sapiens 
2024-12-04 | E-MTAB-14370 | biostudies-arrayexpress
TranscriptomicsGenomic complexity of urothelial bladder cancer revealed in urinary cfDNA
Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.
ORGANISM(S): Homo sapiens 
2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress
GenomicsFragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA
Fragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA
PRJNA1308110 | ENA
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