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A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

OBJECTIVE: The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybri...

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Detalles Bibliográficos
Autores principales: Hasegawa, Keita, Nakabayashi, Kazuhiko, Ishiwata, Keisuke, Kasuga, Yoshifumi, Hata, Kenichiro, Tanaka, Mamoru
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326935/
https://www.ncbi.nlm.nih.gov/pubmed/37415255
http://dx.doi.org/10.1186/s13104-023-06401-3
Descripción
Sumario:OBJECTIVE: The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybridization capture and TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine. RESULTS: We compared a publicly available dataset generated by the standard Agilent protocol of SureSelect XT Human Methyl-Seq Kit and our dataset obtained by our modified protocol, EMCap, that adopted sample pre-pooling and enzymatic conversion. We confirmed that the quality of DNA methylation data was comparable between the two datasets. As our protocol, EMCap, is more cost-effective and reduces the amount of input genomic DNA, it would serve as a better choice for clinical methylome sequencing. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-023-06401-3.