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AMED-CREST Data

We have performed epigenomic analysis including whole-genome bisulfite sequencing (WGBS),
chromatin immunoprecipitation (ChIP-seq), and deep sequencing of mRNAs (RNA-seq).
These reference epigenomes have been registered in IHEC reference registry of epigenomes (EpiRR).

Summary of EpiRR

Publications

Team Kanai

  • Miura F, Enomoto Y, Dairiki R, Ito T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. (2012) 40: e136.
  • Tian Y, Arai E, Gotoh M, Komiyama M, Fujimoto H, Kanai Y. Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes. BMC Cancer. (2014) 14, 772.

Team Shirahige

  • Nakato R, Itoh T, Shirahige K. DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes to Cells. (2013) 18, 589–601.
  • Saito Y, Tsuji J, Mituyama T. Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions. Nucleic Acids Research. (2014) 42, e45.
  • Nozawa R, Nagao K, Igami K, Shibata S, Shirai N, Nozaki N, Sado T, Kimura H, Obuse C. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. Nat Struct Mol Biol. (2013) 20, 566–573.

Team Sasaki

  • Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta. Am J Hum Genet. (2016) 99, 1045–1058.
  • Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H. Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. BMC Genomics. (2017) 18, 31.