{"id":"hum0069","version":1,"url":"https://humandbs.dbcls.jp/research/hum0069/v1","datePublished":"2016-12-09","versions":[{"version":1,"datePublished":"2016-12-09"}],"title":{"ja":"神経筋疾患、ウイルス性疾患におけるRNA発現プロファイル解析","en":"RNA expression profiling of neuromuscular diseases and viral diseases"},"summary":{"aims":{"ja":"神経疾患患者の脳脊髄液（CSF）および血清中のエクソソーム分画におけるsmall RNA（miRNA）のプロファイリングを次世代シークエンサーを用いて行うことで、有用性の高いバイオマーカーを探索する。","en":"MicroRNAs (miRNAs), particularly those found in human body fluids, have been suggested as potential biomarkers. Among various body fluids, the cerebrospinal fluid (CSF) shows promise as a profiling target for diagnosis and monitoring of neurological diseases. However, relevant genome-scale studies are limited and no studies have profiled exosomal miRNAs in CSF. Therefore, we conducted a next-generation sequencing-based survey of small RNAs in the exosomal and non-exosomal (supernatant) fractions of healthy human CSF as well as serum in each donor. Our data provided the first landscape of small RNAs in CSF exosome."},"methods":{"ja":"腰椎穿刺によりCSFおよび血清を採取し、超遠心法によりエクソソーム分画を分離後Total RNAを抽出した。Small RNAライブラリーはTruSeq Small RNA Library Prep Kit（Illumina社）を用いて作製し、10-30塩基のRNAを解析のターゲットとしてPCR 15サイクルで増幅後、HiSeq 2500（Illumina社）を用いて50 baseを読んだ（single-end）。Small RNAシークエンスデータはBWA（version 0.5.9）を用いてhuman reference genome（hg19）にマッピング、small RNAクラスターのmiRNAへのアノテーションにはmiRbase（version 20）を用いた。また、miRdeep2 package（version 2.0.0.7）の'quantifier.pl'スクリプトを用いたデータ処理、解析もあわせて施行した。","en":"Samples were derived from three donors and subjected to a NGS-based survey. CSF samples were obtained via lumbar puncture, centrifuged to remove contaminating cells. Corresponding serum samples were simultaneously isolated from peripheral blood. Samples were further divided into exosomal and supernatant fractions via ultracentrifugation. Total RNA was isolated from each individual fractionated sample (Qiagen). Small RNA libraries were prepared using a TruSeq Small RNA Library Prep Kit (Illumina). Individual libraries were prepared with unique indexes, pooled and subjected to 50-base reads in single lanes of a HiSeq 2500 system (Illumina). Small RNA sequences were aligned to the human reference genome (hg19) using BWA (version 0.5.9). Small RNA clusters were annotated as miRNAs when their genomic coordinates overlapped with those of miRNAs registered in miRbase (version 20). The number of reads aligned within each individual cluster was normalized to counts per million (CPM) after applying a normalization factor based on the relative log expression method via edgeR. Post-processed reads were also analysed using the script 'quantifier.pl' in the miRdeep2 package (version 2.0.0.7; based on the miRbase database)."},"targets":{"ja":"3名の神経筋疾患患者から得られた脳脊髄液および血清ペア（合計6検体）","en":"CSF and serum samples from three donors (neuromuscular disease patients) were analyzed."},"url":{"ja":[{"url":"https://www.tmd.ac.jp/med/nuro/research.html","text":"https://www.tmd.ac.jp/med/nuro/research.html"}],"en":[{"url":"https://www.tmd.ac.jp/med/nuro/research-e.html","text":"https://www.tmd.ac.jp/med/nuro/research-e.html"}]}},"listingSummary":{"methods":{"ja":"発現","en":"Expression profiling"},"targets":{"ja":"神経筋疾患：3症例\n（日本人）","en":"3 Neuromuscular disease (control group)\n(Japanese)"},"typeOfData":{"ja":"NGS\n（small RNA-seq）","en":"NGS\n(small RNA-seq)"}},"releaseNote":{"ja":"神経筋疾患3症例から採取した脳脊髄液および血清ペア（合計6検体）から抽出したtotal RNAを使用し、small RNA-seq解析した結果をFastqファイルにて提供する。TruSeq Small RNA Library Prep Kit（Illumina社）によるmiRNAライブラリ作製後、10-30塩基のRNAをターゲットとしてHiSeq 2500にて平均長50ベースを読んだ（single-end）。","en":"Total RNAs extracted from CSF and serum samples from three donors (neuromuscular disease patients) were used for the small RNA-seq (Fastq files).\nSmall RNA libraries were prepared using a TruSeq Small RNA Library Prep Kit (Illumina) and subjected to 50-base reads in single lanes of a HiSeq 2500 system (Illumina)."},"dataProviders":[{"name":{"ja":"横田 隆徳","en":"Takanori Yokota"},"organization":{"name":{"ja":"東京医科歯科大学大学院 脳神経病態学分野（神経内科）","en":"Tokyo Medical and Dental University, Department of Neurology and Neurological Science"}}}],"researchProjects":[{"name":{"ja":"体液中マイクロRNA測定技術基盤開発プロジェクト","en":"Development of Diagnostic Technology for Detection of miRNA in Body Fluids"},"url":{"ja":[{"url":"https://www.tmd.ac.jp/med/nuro/research.html","text":"https://www.tmd.ac.jp/med/nuro/research.html"}],"en":null}}],"grants":[{"title":{"ja":"体液中マイクロRNA測定技術基盤開発","en":"Development of Diagnostic Technology for Detection of miRNA in Body Fluids"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代治療・診断実現のための創薬基盤技術開発事業 / 新エネルギー・産業技術総合開発機構（NEDO）","en":"Project Focused on Developing Key Technology for Discovering and Manufacturing Drugs for Next-Generation Treatment and Diagnosis, Japan Agency for Medical Research and Development (AMED) / New Energy and Industrial Technology Development Organization (NEDO)"},"grantIds":["JP16ae0101016"]}],"relatedPublications":[{"title":"Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes.","doi":"https://doi.org/10.1016/j.neulet.2016.10.042","datasets":["JGAD000064"]}],"datasets":["JGAD000064"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Ana Aransay"},"affiliation":{"en":"Genome Analysis Platform, CIC bioGUNE"},"country":{"ja":"スペイン","en":"Spain"},"researchTitle":{"ja":"Non-invasive diagnosis of Pediatric Medulloblastoma","en":"Non-invasive diagnosis of Pediatric Medulloblastoma"},"periodStart":"2018-12-18","periodEnd":"2019-09-23","datasets":["JGAD000064"]},{"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":["JGAD000064"]}]}