{"id":"hum0056","version":1,"url":"https://humandbs.dbcls.jp/research/hum0056/v1","datePublished":"2018-03-30","versions":[{"version":1,"datePublished":"2018-03-30"}],"title":{"ja":"ヒト全ゲノム解析に基づく高精度の住民ゲノム参照パネルと3層オミックスパネルの作成","en":"Genome and Multi-layer omics reference panels using blood samples from a population-based cohort study"},"summary":{"aims":{"ja":"いわて東北メディカル・メガバンク機構（IMM）が実施した多層オミックス参照パネルを研究コミュニティに提供すること。","en":"To provide genome and multi-layer omics data from a population based cohort (Iwate Medical Megabank: IMM) to research communities"},"methods":{"ja":"東北メディカル・メガバンク計画地域住民コホート参加者197名のバフィーコートもしくは末梢血より単離した単球、CD4陽性Tリンパ球、好中球を対象に、次世代シークエンサーによる全ゲノムシークエンス（Whole Genome Sequencing: WGS）、全ゲノムバイサルファイトシークエンス（Whole Genome Bisulfite Sequencing: WGBS）およびRNA シークエンス（RNA Sequencing: RNA-seq）を実施した。197名のSNPsのアリル頻度情報、CpG部位のメチル化率情報、各転写物のFPKM値情報を提供する。","en":"Allele frequencies based on whole genome sequencing (WGS), methylation rates based on whole genome bisulfite sequencing (WGBS), and FPKM values based on RNA sequencing (RNA-seq) of 102 monocytes, 102 CD4+ T cells, and 94 neutrophils (total 197 individuals from IMM cohort) isolated from peripheral blood cells."},"targets":{"ja":"IMM地域住民コホート102名の単球、102名のCD4陽性Tリンパ球、94名の好中球（計：197名）","en":"Monocytes and CD4+ T cells from 102 individuals, and neutrophils from 94 individuals in each (total 197 individuals)"},"url":{"ja":[{"url":"https://imethyl.iwate-megabank.org/","text":"https://imethyl.iwate-megabank.org/"}],"en":[{"url":"https://imethyl.iwate-megabank.org/","text":"https://imethyl.iwate-megabank.org/"}]}},"listingSummary":{"methods":{"ja":"配列決定\nメチル化\n発現","en":"Sequencing, methylation profiling, expression profiling"},"targets":{"ja":"197名\n（日本人）","en":"197 participants\n(Japanese)"},"typeOfData":{"ja":"NGS\n（WGS、WGBS、RNA-seq）","en":"NGS\n(WGS, WGBS, RNA-seq)"}},"releaseNote":{"ja":"IMM地域住民コホート197名の末梢血より単離した102名の単球、102名のCD4陽性Tリンパ球、および94名の好中球より抽出したDNA・RNAを対象にWGS、WGBS、RNA-seqを実施し、以下の結果についてtxt形式にて提供する。\n（1） WGSからのSNPsの遺伝子型頻度情報\nTruSeq DNA PCR-Free HT Sample Prep Kitによりライブラリを作製し、Illumina [HiSeq 2500およびHiSeq X]にて平均162bpもしくは150bpの断片を解読し（Paired-end）、1%よりも頻度の高い一塩基多型のアリル頻度情報を提供する。\n（2） WGBSからの各CpG部位の平均メチル化率情報\nTruSeq DNA Methylation Kitによりライブラリを作製し、Illumina [HiSeq 2500]にて平均125bpの断片を解読し（Paired-end）、NovoMethyl（ver.0.1.19）によりメチル化率を算出した結果を提供する。\n（3） RNA-seqからの平均FPKM値\nTruSeq RNA Library Preparation Kit v2によりライブラリを作製し、Illumina [HiSeq 2500]にて平均125bpの断片を解読し（Single-end）、遺伝子毎のFPKM値を算出した結果を提供する。","en":"This article provides following analisys results about gDNAs and RNA extracted from high quality purified monocytes, CD4+ T cells, and neutrophil from 197 participants\n(1) Allele Frequencies from WGS\nMultiplex sequence was performed with Illumina [HiSeq 2500/HiSeq X] (162 bp or 150 bp, Paired-end) after library preparation by using of TruSeq DNA PCR-Free HT Sample Prep Kit. Allele counts of SNPs more than 1 are provided (txt file).\n(2) Methylation Rate at each CpG site from WGBS\nMultiplex sequence was performed with Illumina [HiSeq 2500] (125 bp, Paired-end) after library preparation by TruSeq DNA Methylation Kit. Methylation Rates at each CpG site are provided (txt file).\n(3) Average of FPKM value from RNA-seq\nMultiplex sequence was performed with Illumina [HiSeq 2500] (125 bp, Single-end) after library preparation by TruSeq RNA Library Preparation Kit v2. Averages of FPKM values for each gene are provided (txt file)."},"dataProviders":[{"name":{"ja":"清水 厚志","en":"Atsushi Shimizu"},"organization":{"name":{"ja":"岩手医科大学 災害復興事業本部","en":"Disaster Reconstruction Center, Iwate Medical University"}}}],"researchProjects":[{"name":{"ja":"いわて東北メディカル・メガバンク機構 (http://iwate-megabank.org/) /生体情報解析部門","en":"Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization"},"url":{"ja":null,"en":null}}],"grants":[{"title":{"ja":"東北メディカル・メガバンク計画（岩手医科大学）東日本大震災復興特別会計分","en":"Tohoku Medical Megabank Project (Iwate Medical University) Special Account of the Great East Japan Earthquake Disaster Recovery"},"agency":{"ja":"日本医療研究開発機構 医療研究開発推進事業費補助金","en":"Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP18km0105003"]},{"title":{"ja":"東北メディカルメガバンク計画","en":"Tohoku Medical Megabank Project"},"agency":{"ja":"文部科学省 次世代医療研究開発拠点形成事業費補助金","en":"Ministry of Education, Culture, Sports, Science and Technology Japan"},"grantIds":null}],"relatedPublications":[{"title":"Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies","doi":"https://doi.org/10.1038/s41525-017-0016-5","datasets":null}],"datasets":["NHA000067","NHA000065","NHA000066"],"controlledAccessUsers":[]}