{"entity": "researcher", "timestamp": "2026-10-01T11:58:29.042Z", "family": "Han", "given": "Yanan", "initials": "Y", "orcid": "0000-0002-3464-2656", "affiliations": ["Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c15311f230774fe187ea68682c5a4fff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c15311f230774fe187ea68682c5a4fff"}}, "publications": [{"entity": "publication", "iuid": "0e77424fabfa4d3eade0a77a33931009", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0e77424fabfa4d3eade0a77a33931009.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0e77424fabfa4d3eade0a77a33931009"}}, "title": "Comparison of EM-seq and PBAT methylome library methods for low-input DNA.", "authors": [{"family": "Han", "given": "Yanan", "initials": "Y", "orcid": "0000-0002-3464-2656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c15311f230774fe187ea68682c5a4fff.json"}}, {"family": "Zheleznyakova", "given": "Galina Yurevna", "initials": "GY"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Kakhki", "given": "Majid Pahlevan", "initials": "MP"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "17", "issue": "10", "pages": "1195-1204", "issn-l": "1559-2294"}, "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.", "doi": "10.1080/15592294.2021.1997406", "pmid": "34709110", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9542412"}], "notes": [], "created": "2026-09-23T08:33:06.202Z", "modified": "2026-09-23T08:33:06.344Z"}]}