| Autor: |
Foox, J., Nordlund, J., Lalancette, C., Gong, T., Lacey, M., Lent, S., Langhorst, B.W., Ponnaluri, V.K.C., Williams, L., Padmamabhan, K., Cavalcante, R., Lundmark, A., Butler, D., Gurvitch, J., Greally, J.M., Suzuki, M., Menor, M., Nasu, M., Alonso, A., Sheridan, C., Scherer, A., Bruinsma, S., Golda, G., Muszynska, A., Labaj, P.P., Campbe, M.A., Wos, F., Raine, A., Liljedahl, U., Axelsson, T., Wang, C., Chen, Z., Yang, Z., Li, J., Yang, X., Wang, H., Melnick, A., Guo, S., Blume, A., Franke, V., Ibanez de Caceres, I., Rodriguez-Antolin, C., Rosas, R., Wade Davis, J., Ishii, J., Megherbi, D.B., Xiao, W., Liao, W., Xu, J., Hong, H., Ning, B., Tong, W., Akalin, A., Wang, Y., Mason, C.E. |
| Jazyk: |
angličtina |
| Rok vydání: |
2021 |
| Předmět: |
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| Popis: |
Detection of DNA cytosine modifications such as 5-methylcytosine (5mC) and 5-hydroxy-methylcytosine (5hmC) is essential for understanding the epigenetic changes that guide development, cellular lineage specification, and disease. The wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These genomes were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories. Our primary focus was on cytosine modifications found in mammalian genomes (5mC, 5hmC). Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS, SPLAT), oxidative bisulfite sequencing (oxBS), Enzymatic Methyl-seq (EM-seq), Illumina EPIC targeted-methylation sequencing, and ATAC-seq. Each library was sequenced to high coverage on an Illumina NovaSeq 6000. The data were subject to rigorous quality assessment and subsequently compared to Illumina EPIC methylation microarrays. We provide a wide range of sequence data for commonly used genomics reference materials, as well as best practices for epigenomics research. These findings can serve as a guide for researchers to enable epigenomic analysis of cellular identity in development, health, and disease. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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