{"id":"hum0350","version":1,"url":"https://humandbs.dbcls.jp/research/hum0350/v1","datePublished":"2024-06-13","versions":[{"version":1,"datePublished":"2024-06-13"}],"title":{"ja":"ヒト遺伝子多型とオミックスデータの統合解析のための基盤構築研究","en":"Research to establish a foundation for integrated analysis of human genetic polymorphisms and omics data"},"summary":{"aims":{"ja":"多因子疾患の中で、免疫系が関与する疾病（自己免疫疾患、アレルギー疾患、感染症、癌、移植など）には適切な治療が少ない疾病が多い。この問題を解決し、よりよい治療法を見つけ出すために、ヒト免疫機能の十分な理解と疾患における病態の適切な把握が必要である。本研究では、健常人由来のリンパ球など免疫担当細胞を対象としたオミックス解析と遺伝子多型解析をベースにした新しい疾病研究の方法論を確立し、病態の理解と創薬の標的確定に重要な情報を蓄積する。そのための基盤データとして、健常人における免疫担当細胞のそれぞれのサブセットにおける、遺伝子発現を中心としたオミックス解析を遂行する。","en":"Among multifactorial diseases, there are many diseases involving the immune system (e.g., autoimmune diseases, allergic diseases, infectious diseases, cancer, and transplantation) for which there are few appropriate treatments. In order to solve these problems and find better treatments, we believe that a thorough understanding of human immune functions and an appropriate understanding of pathological conditions in these diseases are necessary. Therefore, this study aims to establish a new methodology for disease research based on omics analyses and genetic polymorphism analysis of immune cells such as lymphocytes derived from healthy individuals, and to accumulate important information for understanding pathological conditions and determining targets for drug discovery."},"methods":{"ja":"健常者3名の全血から単離したCD4陽性T細胞から抽出したRNAまたはDNAに対して5' single-cell RNA-seq、3' single-cell RNA-seq、Micro-C、Region Capture Micro-C、CITE-seq、Multimodal assay（single-nucleus ATAC-seq、 3' and 5' single-nucleus RNA-seq、 5' single-cell RNA-seq）、MAS-seq、CAGE-seq、NET-CAGE-seq を実施した。CRISPR-activated Jurkat cellsから抽出したRNAに対してCAGE-seq を実施した。","en":"5' and 3' single-cell RNA-seq, Micro-C and Region Capture Micro-C, CITE-seq and 5' single-cell RNA-seq, Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq, MAS-seq, CAGE-seq, and NET-CAGE-seq were performed on CD4 positive T cells isolated from whole blood of three healthy Japanese. CAGE-seq was performed on CRISPR-activated Jurkat cells."},"targets":{"ja":"日本人健常者3名（男性1名、女性2名）、CRISPR-activated Jurkat cells","en":"Three healthy Japanese (one male, two females), CRISPR-activated Jurkat cells"},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"発現\n転写開始点同定","en":"Expression profiling, Transcription start site identification"},"targets":{"ja":"健常者：3名\n（男性：1名、女性：2名）\n（日本人）\nCRISPR-activated Jurkat cells：15検体\n（細胞株）","en":"3 healthy individuals (1 male, 2 females)\n(Japanese)\nCRISPR-activated Jurkat cells: 15 samples\n(Cell-line)"},"typeOfData":{"ja":"NGS\n（5' single-cell RNA-seq、3' single-cell RNA-seq、Micro-C and Region Capture Micro-C、CITE-seq、Multimodal assay（single-nucleus ATAC-seq、 3' and 5' single-nucleus RNA-seq、 5' single-cell RNA-seq）、MAS-seq、CAGE-seq、NET-CAGE-seq）","en":"NGS\n(5' single-cell RNA-seq, 3' single-cell RNA-seq, Micro-C and Region Capture Micro-C, CITE-seq, Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq, MAS-seq, CAGE-seq, and NET-CAGE-seq)"}},"releaseNote":{"ja":"日本人健常者3名（男性1名、女性2名）の全血から単離したCD4陽性T細胞から抽出したRNAまたはDNAに対して実施した、5' single-cell RNA-seq、3' single-cell RNA-seq、Micro-C and Region Capture Micro-C、CITE-seq、Multimodal assay（single-nucleus ATAC-seq、 3' and 5' single-nucleus RNA-seq、 5' single-cell RNA-seq）、MAS-seq、CAGE-seq、NET-CAGE-seq解析、ならびに、CRISPR-activated Jurkat cellsから抽出したRNAに対して実施したCAGE-seq解析データをfastq、bed、matrix、tsv、GTFファイルにて提供する。","en":"5' and 3' single-cell RNA-seq, Micro-C and Region Capture Micro-C, CITE-seq and 5' single-cell RNA-seq, Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq, MAS-seq, CAGE-seq, and NET-CAGE-seq were performed on CD4 positive T cells isolated from whole blood of three healthy Japanese. CAGE-seq was performed on CRISPR-activated Jurkat cells. Fastq, bed, matrix, tsv and GTF files are provided."},"dataProviders":[{"name":{"ja":"山本 一彦","en":"Kazuhiko Yamamoto"},"organization":{"name":{"ja":"理化学研究所 生命医科学研究センター 自己免疫疾患研究チーム","en":"Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences"}}}],"researchProjects":[],"grants":[{"title":{"ja":"多因子疾患における疾患リスク遺伝子多型を用いた病態解析に関する新しい方法論の確立","en":"Establishment of a novel strategy for pathological analysis of multifactorial diseases using genetic risk variants"},"agency":{"ja":"科学研究費助成事業 基盤研究（S）","en":"KAKENHI Grant-in-Aid for Scientific Research (S)"},"grantIds":["18H05285"]},{"title":{"ja":"遺伝的多様性と機能に関するマルチオミックスを中心としたヒト免疫評価法の確立と支援の為のサポート機関","en":"Support institute for vaccine development by functional evaluation of human immune system through integration of genetic variations and multi-omics data"},"agency":{"ja":"日本医療研究開発機構（AMED） ワクチン開発のための世界トップレベル研究開発拠点の形成事業","en":"Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP223fa627010"]}],"relatedPublications":[{"title":"An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases","doi":"https://doi.org/10.1126/science.add8394","datasets":["JGAD000822","DRA018405","E-GEAD-739","E-GEAD-740","E-GEAD-741","E-GEAD-742","E-GEAD-743","E-GEAD-744","E-GEAD-745","E-GEAD-746"]}],"datasets":["JGAD000822","E-GEAD-741","E-GEAD-742","E-GEAD-743","E-GEAD-744","E-GEAD-746","E-GEAD-745","E-GEAD-740","DRA018405","E-GEAD-739"],"controlledAccessUsers":[]}