{"id":"hum0091","version":1,"url":"https://humandbs.dbcls.jp/research/hum0091/v1","datePublished":"2021-03-12","versions":[{"version":1,"datePublished":"2021-03-12"}],"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（GACシリーズ）","en":"Study of molecular-genetics, and molecular epidemiology for developing treatment of esophageal cancer (GAC 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":"胃粘膜から腺管分離法で純化した表層粘液細胞 （腺窩上皮細胞）を対象とするChIP-seq解析、RNA-seq解析、PBAT-seq解析","en":"ChIP-Seq, RNA-seq and PBAT-seq analysis about normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method."},"targets":{"ja":"胃粘膜から腺管分離法で純化した表層粘液細胞 （腺窩上皮細胞） 14種類（正常： 14検体）","en":"Normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method : 14 cells"},"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"},"targets":{"ja":"胃粘膜表層粘液細胞：14種類\n（日本人）","en":"14 Normal human foveolar epithelial cells of the stomach\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胃粘膜から腺管分離法で純化した表層粘液細胞 （腺窩上皮細胞）より抽出したDNAを用いたPBAT-seq解析の結果を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胃粘膜から腺管分離法で純化した表層粘液細胞 （腺窩上皮細胞）より抽出したDNAを用いたChIP-seq解析の結果を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 2500（Illumina）によりシークエンシング行っている。\nNGS（RNA-seq）\n胃粘膜から腺管分離法で純化した表層粘液細胞 （腺窩上皮細胞）より抽出したRNAを用いたRNA-seq解析の結果をfastqファイルにて提供する。Agilent SureSelect Strand Specific RNA kitによるライブラリ作製、Hiseq2000(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 human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method 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 provided Dr. Hiroshi Kimura, Tokyo Institute of Technology, were used for immunoprecipitation. ChIP-Seq libraries were sequenced using the HiSeq 2500 (Illumina) platform.\nNGS (RNA-seq)\nTotal RNAs extracted from normal human foveolar epithelial cells of the stomach purified from gastrectomy specimens using crypt isolation method were used for whole transcriptome-sequencing analysis (fastq format files). cDNAs were prepared using the Agilent SureSelect Strand Specific RNA kit 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":[],"datasets":["JGAD000082","JGAD000243","JGAD000081"],"controlledAccessUsers":[{"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":["JGAD000081"]}]}