{"id":"NHA000004","research":"hum0009","url":"https://humandbs.dbcls.jp/dataset/NHA000004","datePublished":"2015-01-07","dateModified":"2015-01-07","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"unrestricted-access","label":{"ja":"非制限公開","en":"Unrestricted-access"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"CpGサイトのメチル化率情報","en":"methylation rate at each CpG site"}}],"experiments":[{"label":"PBAT-seq (DNA メチル化解析)","values":[{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":11,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"sample","label":{"ja":"検体数","en":"Sample"}}]},{"key":"sex","label":{"ja":"性別","en":"Sex"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"key":"age-group","label":{"ja":"年齢層","en":"Age group"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"oocyte","label":{"en":"Oocyte"}},{"code":"sperm","label":{"en":"Sperm"}},{"code":"embryo","label":{"en":"Embryo"}},{"code":"cord-blood","label":{"ja":"臍帯血","en":"Cord blood"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"normal","label":{"ja":"非腫瘍","en":"Normal"}}]},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"methyl-seq","label":{"en":"Methyl-seq"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"末端4塩基をトリム後、Bismark（v.0.9.0）のデフォルトパラメータを使用してアライメントを実施した。","en":"Sequenced reads were processed using the Illumina standard base-calling pipeline (v1.8.2) and the first 4 bases were trimmed to remove random primer sequences. The resulting reads were aligned to the reference genome (UCSC hg19) using Bismark (v.0.9.0) with default parameters."}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"バイサルファイト変換効率＞99％（λファージゲノムを使用）","en":"Bisulfite conversion rates were estimated using reads that uniquely aligned to the lambda phage genome and were >99% for all samples."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Bismark（v.0.9.0）のmethylation extractorを使用し、各シトシンのメチル化率を算出。CpGサイトについては、両ストランドのリードを合わせてメチル化率を算出した。","en":"The methylation level of each cytosine was calculated using the Bismark methylation extractor. For CpG sites, reads from both strands were combined to calculate the methylation levels."}},{"key":"read-count","label":{"ja":"リード数","en":"Read count"},"type":"text","text":{"ja":"卵子（増幅有）：752 million reads / 144 million reads\n卵子（増幅無）：153 million reads / 80 million reads\n精子-1：392 million reads / 243 million reads\n精子-2：457 million reads / 259 million reads\n精子-3：450 million reads / 281 million reads\n受精卵（着床前胚）：1275 million reads / 750 million reads\n臍帯血-1：181 million reads / 102 million reads\n臍帯血-2：185 million reads / 108 million reads\n臍帯血-3：177 million reads / 98 million reads\n臍帯血-4：179 million reads / 101million reads\n臍帯血-5：196 million reads / 114 million reads","en":"Oocyte-1: 752 million reads / 144 million reads\nOocyte-2: 153 million reads / 80 million reads\nSperm-1: 392 million reads / 243 million reads\nSperm-2: 457 million reads / 259 million reads\nSperm-3: 450 million reads / 281 million reads\nPreimplantation embryos: 1275 million reads / 750 million reads\nCord blood cells-1: 181 million reads / 102 million reads\nCord blood cells-2: 185 million reads / 108 million reads\nCord blood cells-3: 177 million reads / 98 million reads\nCord blood cells-4: 179 million reads / 101million reads\nCord blood cells-5: 196 million reads / 114 million reads"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":4.5,"unit":"x","high":null,"prefix":{"ja":"卵子(増幅有): ","en":"Oocyte-1 (amplified): "}},{"value":2.5,"unit":"x","high":null,"prefix":{"ja":"卵子(増幅無): ","en":"Oocyte-2 (not amplified): "}},{"value":7.6,"unit":"x","high":null,"prefix":{"ja":"精子-1: ","en":"Sperm-1: "}},{"value":8.1,"unit":"x","high":null,"prefix":{"ja":"精子-2: ","en":"Sperm-2: "}},{"value":8.8,"unit":"x","high":null,"prefix":{"ja":"精子-3: ","en":"Sperm-3: "}},{"value":23.5,"unit":"x","high":null,"prefix":{"ja":"受精卵(着床前胚): ","en":"Preimplantation embryos: "}},{"value":3.2,"unit":"x","high":null,"prefix":{"ja":"臍帯血-1: ","en":"Cord blood cells-1: "}},{"value":3.4,"unit":"x","high":null,"prefix":{"ja":"臍帯血-2: ","en":"Cord blood cells-2: "}},{"value":3.1,"unit":"x","high":null,"prefix":{"ja":"臍帯血-3: ","en":"Cord blood cells-3: "}},{"value":3.2,"unit":"x","high":null,"prefix":{"ja":"臍帯血-4: ","en":"Cord blood cells-4: "}},{"value":3.6,"unit":"x","high":null,"prefix":{"ja":"臍帯血-5: ","en":"Cord blood cells-5: "}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"dna-methylation-data","label":{"ja":"DNA メチル化データ","en":"DNA methylation data"}}]},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"zip","label":{"en":"ZIP"}}]}