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19552e24-c61b-4053-a9b9-3e6ce25dc1d1 - samples

ABSTRACT: 5 human plasma cell-free DNA cases (BS-seq)

PROVIDER: EGAD00001008809 | EGA |

REPOSITORIES: EGA

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Project description:cell-free DNA sequencing of plasma

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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

ecdfede6-064a-4136-91b2-adb305553e34 - samples

Project description:Consists of 76 mouse plasma cell-free DNA, 30 mouse Liver DNA, 10 human plasma cell-free DNA

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H3K4me3 and YY1 ChIP-seq of untreated 2102Ep cells

Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1) in the genome of 2102Ep cells (E-MTAB-10895). We also achieved targeted nanopore sequencing to assay DNA methylation over a subset of loci (E-MTAB-12247). To further study the link between L1 DNA methylation and expression, we performed, in the same cell line, RNA-seq (E-MTAB-12246), as well as YY1 and H3K4me3 ChIP-seq (this dataset).

2023-09-23 | E-MTAB-12249 | biostudies-arrayexpress

77a48f6f-821b-4f78-bcbb-945fbf605a3f - samples

Project description:36 mouse plasma cell-free DNA cases

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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

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RNA-seq of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine

Project description:We performed poly(A)+ stranded RNA-seq of a panel of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine. In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same samples using bs-ATLAS-seq (E-MTAB-12240). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12245 | biostudies-arrayexpress

RNA-seq of a panel of human normal and cancer cell lines

Project description:We performed poly(A)+ stranded RNA-seq of a panel of human primary or transformed cell lines (BJ, IMR90, MRC5, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep). In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same cell lines using bs-ATLAS-seq (E-MTAB-10895). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12246 | biostudies-arrayexpress

Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq

Project description:Three separate experiments were carried out using MeDIP-seq and cfMeDIP-seq for methylome analysis. For the first experiment, different starting amounts of HCT116 cell line DNA, sheared to mimic cell-free DNA, were analyzed using MeDIP-seq and cfMeDIP-seq. In the second experiment the limit of detection of cfMeDIP-seq was tested using varying dilutions of colorectal cancer cell line DNA (HCT116) with multiple myeloma cell line DNA (MM1.S). For both cell line DNA samples, the DNA was sheared to mimic cell-free DNA. In the final experiment, we tested the enrichment of human ctDNA using cfMeDIP-seq performed on plasma collected from patient-derived xenografts (PDXs) generated in mice from two colorectal cancer patients.

2018-04-01 | GSE79838 | GEO

aa5fdd2f-4b4a-4ab1-b1fb-fa0fe94e1180 - samples

Project description:Heatrich-BS was performed on 5 healthy volunteers and 15 CRC patient cell-free DNA. The Heatrich-BS predicted tumor fractions were compared with tumor burden values obtained by genomic methods such as targeted amplicon sequencing and low pass sequencing.

| EGAD00001008715 | EGA

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