ArticleEpigenetics2022
Comparison of EM-seq and PBAT methylome library methods for low-input DNA.
Article in Epigenetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- 5mC and 5hmC methylation sequencing: the power of 6-base sequencing in a multiomic era.Epigenomics · 2026Review
- Laser Capture Microdissection Followed by DNA Methylation Profiling.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Associations Between Non-Genetic Risk Factors and DNA Methylation Alterations in Barrett's Esophagus and Its Progression to Esophageal Adenocarcinoma.International journal of molecular sciences · 2025Review
- An optimized protocol to detect high-throughput DNA methylation from custom targeted sequences on 96 samples simultaneously.FEBS open bio · 2025Article
- Pan-Cancer Detection Through DNA Methylation Profiling Using Enzymatic Conversion Library Preparation with Targeted Sequencing.International journal of molecular sciences · 2025Article
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Comparison of current methods for genome-wide DNA methylation profiling.Epigenetics & chromatin · 2025Article
- Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.Heredity · 2025Article
- T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis.Cell reports. Medicine · 2025Article
- DNA methylation in esophageal cancer: technological advances and early detection clinical applications.Frontiers in oncology · 2025Review
- Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling.Frontiers in epigenetics and epigenomics · 2025Article
- Whole Genome Methylation Sequencing via Enzymatic Conversion (EM-seq): Protocol, Data Processing, and Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Whole genome methylation sequencing in blood from persons with mild cognitive impairment and dementia due to Alzheimer's disease identifies cognitive status.bioRxiv : the preprint server for biology · 2024Article
- DNA methylation of exercise-responsive genes differs between trained and untrained men.BMC biology · 2024Article
- Novel genome-wide DNA methylation profiling reveals distinct epigenetic landscape, prognostic model and cellular composition of early-stage lung adenocarcinoma.Journal of translational medicine · 2024Article
- Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late-onset dementia due to Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for the detection of the 5mC sites in cancer and normal samples.Frontiers in epigenetics and epigenomics · 2024Article
- Novel urine cell-free DNA methylation markers for hepatocellular carcinoma.Scientific reports · 2023Article
- Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network.Genome medicine · 2023Article
- A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion.BMC research notes · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.
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