{"id":"hum0032","version":1,"url":"https://humandbs.dbcls.jp/research/hum0032/v1","datePublished":"2016-07-22","versions":[{"version":1,"datePublished":"2016-07-22"}],"title":{"ja":"ヒト消化器ならびに泌尿器上皮細胞の標準エピゲノム解析（HPCシリーズ）","en":"Standard epigenome mapping in human epithelial cells of the digestive and urogenital organs (HPC series)"},"summary":{"aims":{"ja":"国際ヒトエピゲノムコンソーシアム（The International Human Epigenome Consortium: IHEC）に参画し、年齢・性別の異なる複数の日本人検体から得られた正常細胞等の高品質な標準エピゲノムプロファイルを取得し、データを広く公開して研究基盤形成に貢献する。","en":"The aim of this study is to participate in International Human Epigenome Consortium (http://ihec-epigenomes.org/), through disclosure of quality reference epigenome profiles in normal and diseased cells obtained from multiple Japanese people."},"methods":{"ja":"肝部分切除術検体から純化した肝細胞を対象とするPBAT-seq解析、ChIP-seq解析、RNA-seq解析","en":"ChIP-Seq, RNA-seq and PBAT-seq analysis about normal and diseased human hepatocytes purified from partial hepatectomy specimens."},"targets":{"ja":"肝部分切除術検体から純化した肝細胞 8種類（正常：6例、B型肝炎ウイルス感染陽性：1症例、C型肝炎ウイルス感染陽性：1症例）","en":"Normal and diseased human hepatocytes purified from partial hepatectomy specimens (normal human hepatocytes: 6, hepatitis B virus (HBV)-positive human hepatocyte 1 and hepatitis C virus (HCV)-positive human hepatocyte 1."},"url":{"ja":null,"en":[{"url":"https://crest-ihec.jp/english/project/index.html","text":"https://crest-ihec.jp/english/project/index.html"}]}},"listingSummary":{"methods":{"ja":"発現\nメチル化\nヒストン修飾","en":"Expression profiling, methylation profiling, histone modification profiling"},"targets":{"ja":"肝細胞：8種類\n（日本人）","en":"8 partial hepatectomy specimens\n(Japanese)"},"typeOfData":{"ja":"NGS\n（PBAT-seq、ChIP-seq、RNA-seq）","en":"NGS\n(PBAT-seq, ChIP-seq, RNA-seq)"}},"releaseNote":{"ja":"NGS（PBAT-seq）\n肝部分切除術検体から純化した肝細胞から抽出したDNAを用いWGBS解析した結果をFastqファイルにて提供する。Post-Bisulfite Adaptor-Tagging（PBAT）法（http://crest-ihec.jp/epigenome/index.html）でライブラリ作製し、HiSeq 2000（Illumina）によりシングルエンドシークエンシングを行っている。\nNGS（ChIP-seq）\n肝部分切除術検体から純化した肝細胞から抽出したDNAを用いChIP-seq解析した結果をFastqファイルにて提供する。抗H3K4me3,H3K9me3, H3K27me3, H3K27ac, H3K4me1, H3K36me3モノクローナル抗体（東京工業大学木村宏教授提供）を用いて免疫沈降後ChIP-Seqライブラリを作製し、HiSeq 2000もしくは2500（Illumina）によりシークエンシング行っている。\nNGS（RNA-seq）\n肝部分切除術検体から純化した肝細胞から抽出したDNAを用いRNA-seq解析した結果をFastqファイルにて提供するIllumina TruSeq RNA Library Preparation Kit v2 ないし Agilent SureSelect Strand Specific RNA kitによるライブラリ作製、HiSeq 2000（Illumina）での100bpペアエンドシークエンシングを行っている。","en":"NGS (PBAT-seq)\ngDNAs extracted from normal and diseased human hepatocytes purified from partial hepatectomy specimens were used for analyses (fastq format files). After library preparation by post-bisulfite adaptor-tagging (PBAT, http://crest-ihec.jp/english/epigenome/index.html) and multiplex sequence was performed with the Illumina HiSeq 2000 sequencer (100 bp, Single-end).\nNGS (ChIP-seq)\nAnti H3K4me3,H3K9me3, H3K27me3, H3K27ac, H3K4me1 and H3K36me3 mouse monoclonal antibodies, kindly provied Dr. Hiroshi Kimura, Tokyo Institute of Technology, were used for immunoprecipitation. ChIP-Seq libraries were sequenced using the HiSeq 2000 or 2500 (Illumina) platform.\nNGS (RNA-seq)\nTotal RNAs extracted from normal and diseased human hepatocytes purified from partial hepatectomy specimens were used for whole transcriptome-sequencing analysis (fastq format files). cDNAs were prepared using the TruSeq RNA Library Preparation Kit v2 (Illumina) or SureSelect Strand Specific RNA kit (Agilent) and multiplex sequence was performed with the Illumina HiSeq 2000 sequencer (100 bp, Paired-end)."},"dataProviders":[{"name":{"ja":"金井 弥栄","en":"Yae Kanai"},"organization":{"name":{"ja":"慶應義塾大学医学部病理学教室","en":"Department of Pathology, Keio University School of Medicine"}}}],"researchProjects":[{"name":{"ja":"革新的先端研究開発支援事業（AMED-CREST） 国際ヒトエピゲノムコンソーシアム（IHEC）金井チーム","en":"AMED-CREST International Human Epigenome Consortium (IHEC) Team Kanai"},"url":{"ja":[{"url":"https://crest-ihec.jp/index.html","text":"https://crest-ihec.jp/index.html"}],"en":[{"url":"https://crest-ihec.jp/english/index.html","text":"https://crest-ihec.jp/english/index.html"}]}}],"grants":[{"title":{"ja":"「エピゲノム研究に基づく診断・治療へ向けた新技術の創出」領域","en":"Development of Fundamental Technologies for Diagnosis and Therapy Based upon Epigenome Analysis"},"agency":{"ja":"日本医療研究開発機構 革新的先端研究開発支援事業（AMED-CREST）","en":"Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST)"},"grantIds":null}],"relatedPublications":[{"title":"Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.","doi":"https://doi.org/10.1093/nar/gks454","datasets":["JGAD000026"]},{"title":"Multilayer-omics analyses of human cancers: exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium.","doi":"https://doi.org/10.3389/fgene.2014.00024","datasets":null}],"datasets":["JGAD000026","JGAD000027","JGAD000028"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Guillaume Bourque"},"affiliation":{"en":"McGill University & Genome Quebec Innovation Center, McGill University"},"country":{"ja":"カナダ (ケベック州)","en":"Quebec, Canada"},"researchTitle":{"ja":"Epigenome Meta-Analysis Project (epiMAP)","en":"Epigenome Meta-Analysis Project (epiMAP)"},"periodStart":"2018-06-07","periodEnd":"2021-03-19","datasets":["JGAD000026","JGAD000027","JGAD000028"]},{"principalInvestigator":{"en":"Martin Hirst"},"affiliation":{"en":"BC Cancer, part of the Provincial Health Services Authority"},"country":{"ja":"カナダ (ブリティッシュコロンビア州)","en":"British Columbia, Canada"},"researchTitle":{"ja":"Epigenomic analysis of human samples","en":"Epigenomic analysis of human samples"},"periodStart":"2018-08-06","periodEnd":"2022-09-05","datasets":["JGAD000026","JGAD000027","JGAD000028"]},{"principalInvestigator":{"en":"Quan Long"},"affiliation":{"en":"Faculty of Medicine, Department of Biochemistry & Molecular Biology, University of Calgary"},"country":{"ja":"カナダ (アルバータ州)","en":"Alberta, Canada"},"researchTitle":{"ja":"Characterizing intrapatient methylome evolution through epihaplotype reconstruction and applied deep learning models.","en":"Characterizing intrapatient methylome evolution through epihaplotype reconstruction and applied deep learning models."},"periodStart":"2019-01-21","periodEnd":"2023-09-21","datasets":["JGAD000026","JGAD000027","JGAD000028"]},{"principalInvestigator":{"en":"Quan Long"},"affiliation":{"en":"Faculty of Medicine, Department of Biochemistry & Molecular Biology, University of Calgary"},"country":{"ja":"カナダ (アルバータ州)","en":"Alberta, Canada"},"researchTitle":{"ja":"Characterizing intrapatient methylome evolution through epihaplotype reconstruction and applied deep learning models.","en":"Characterizing intrapatient methylome evolution through epihaplotype reconstruction and applied deep learning models."},"periodStart":"2019-05-13","periodEnd":"2021-03-19","datasets":["JGAD000027","JGAD000028"]},{"principalInvestigator":{"ja":"浜田 道昭","en":"Michiaki Hamada"},"affiliation":{"ja":"浜田研究室, 理工学術院, 早稲田大学","en":"Hamada Laboratory, Faculty of Science and Engineering, Waseda University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"RNA標的創薬データベースの構築","en":"Construction of RNA-targeted Drug Discovery Database"},"periodStart":"2023-01-05","periodEnd":"2027-10-31","datasets":["JGAD000028"]}]}