{"id":"hum0177","version":1,"url":"https://humandbs.dbcls.jp/research/hum0177/v1","datePublished":"2020-04-27","versions":[{"version":1,"datePublished":"2020-04-27"}],"title":{"ja":"脳腫瘍の悪性化に関与する遺伝子の解析","en":"Genetic analysis assciated with malignance of brain tumor"},"summary":{"aims":{"ja":"H3F3A遺伝子変異をもつ悪性神経膠腫におけるDNAメチル化解析","en":"DNA methylome analyses and expression analysis for malignant glioma harbouring H3F3A gene mutation"},"methods":{"ja":"悪性神経膠腫症例の腫瘍組織から抽出したDNA・RNAを用いたPBAT-seq（14症例＋細胞株1種）、RNA-seq（14症例中の5症例＋細胞株1種）およびChIP-seq（細胞株1種）","en":"PBAT-seq, RNA-seq and ChIP-seq"},"targets":{"ja":"悪性神経膠腫","en":"14 Malignant glioma patients and 1 cell line"},"url":{"ja":null,"en":null}},"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":"悪性神経膠腫：14症例\n（日本人）","en":"14 malignant gliomas\n(Japanese)"},"typeOfData":{"ja":"NGS\n（PBAT-seq、RNA-seq、ChIP-seq）","en":"NGS\n(PBAT-seq, RNA-seq, ChIP-seq)"}},"releaseNote":{"ja":"・PBAT-seq\nこのバージョンでは、悪性神経膠腫14症例の腫瘍組織および細胞株1種から抽出したDNAを用いたPBAT-seq解析の結果をfastqファイルにて提供する。TACS ligation-mediated PBAT（Miura F, Nucleic Acids Res. 2019）によるライブラリ作製後、Hiseq X Ten（Illumina）によりシークエンシングを行っている。\n・RNA-seq\nこのバージョンでは、悪性神経膠腫5症例の腫瘍組織および細胞株1種から抽出したRNAを用いたRNA-seq解析の結果をfastqファイルにて提供する。TruSeq stranded mRNA Kitによるライブラリ作製後、NovaSeq 6000（Illumina）によりシークエンシングを行っている。\n・ChIP-seq\nこのバージョンでは、悪性神経膠腫細胞株1種から抽出したDNAを用いたChIP-seq解析の結果をfastqファイルにて提供する。SMARTer ThruPLEX DNA-seq Kitおよび抗H3.3抗体および抗H3.3 G34V抗体を用いた免疫沈降によりライブラリを作製し、NovaSeq 6000（Illumina）によりシークエンシングを行っている。","en":"- PBAT-seq\nDNAs extracted from tumor tissues of malignant glioma and cell line were used for PBAT-sequencing analysis (fastq format files). Libraries were prepared with TACS ligation-mediated PBAT (Miura F, Nucleic Acids Res. 2019) and sequenced using Hiseq X Ten (Illumina).\n- RNA-seq\nRNAs extracted from tumor tissues of malignant glioma and cell line were used for RNA-sequencing analysis (fastq format files). Libraries were prepared with TruSeq stranded mRNA Kit and sequenced using NovaSeq 6000 (Illumina).\n- ChIP-seq\nDNAs extracted from cell line of malignant glioma were used for ChIP sequencing analysis (fastq format files). Libraries were prepared with SMARTer ThruPLEX DNA-seq Kit. Anti- H3.3 antibody and anti- H3.3 G34V antibody were used for immunoprecipitation. ChIP-Seq libraries were sequenced using NovaSeq 6000 (Illumina)."},"dataProviders":[{"name":{"ja":"伊藤 隆司","en":"Takashi Ito"},"organization":{"name":{"ja":"九州大学大学院医学研究院 医化学分野","en":"Department of Medical Biochemistry, Graduate School of Medical Sciences, Kyushu University"}}}],"researchProjects":[],"grants":[{"title":{"ja":"メチローム解析の高度化と支援","en":"Improvements and support in methylome analysis"},"agency":{"ja":"日本医療研究開発機構（AMED） 創薬等ライフサイエンス研究支援基盤事業","en":"Platform Project for Supporting Drug Discovery and Life Science Research, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP16am0101059"]},{"title":{"ja":"先進メチローム解析の支援と高度化","en":"Advanced methylomics: support and development"},"agency":{"ja":"日本医療研究開発機構（AMED） 創薬等ライフサイエンス研究支援基盤事業","en":"Platform Project for Supporting Drug Discovery and Life Science Research, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP19am0101103"]},{"title":{"ja":"次世代エピゲノム解析技術の開発とその応用","en":"Development and applications of next generation epigenome analysis technologies"},"agency":{"ja":"科学研究費助成事業 新学術領域研究（研究領域提案型）","en":"KAKENHI Grant-in-Aid for Scientific Research on Priority Areas (Research in a proposed research area)"},"grantIds":["17H06305"]}],"relatedPublications":[{"title":"Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging","doi":"https://doi.org/10.1093/nar/gkz435","datasets":null}],"datasets":["JGAD000280","JGAD000281","JGAD000282"],"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":["JGAD000281"]}]}