{"id":"NHA000133","research":"hum0207","url":"https://humandbs.dbcls.jp/dataset/NHA000133","datePublished":"2020-01-06","dateModified":"2020-01-06","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":"NGS（Hi-C）によるループ情報","en":"Loops from NGS (Hi-C)"}}],"experiments":[{"label":"Hi-C","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"関節リウマチ（ICD10：M05）：7症例\n1症例あたり、滑膜線維芽細胞 3条件（無刺激, TNF-α, 8-mix）を用意し、同じ条件のサンプルをプール：計3検体","en":"rheumatoid arthritis (ICD10: M05): 7 case\n3 conditions of synovial fibroblasts (unstimulated, TNF-α, and 8-mix) were prepared for 1 case each. Samples under the same condition were pooled : total 3 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"M05","label":{"ja":"血清反応陽性関節リウマチ","en":"Seropositive rheumatoid arthritis"}}],"name":{"ja":"関節リウマチ","en":"rheumatoid arthritis"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"affected","label":{"ja":"罹患","en":"Affected"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":7,"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":"individual","label":{"ja":"人数","en":"Individual"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"関節リウマチ患者由来の各細胞から抽出したDNA","en":"DNAs extracted from pooled cells from rheumatoid arthritis patient"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"synovial-fibroblast","label":{"en":"Synovial fibroblast"}}]},{"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":"sample-provider","label":{"ja":"試料の入手元","en":"Sample provider"},"type":"text","text":{"ja":null,"en":null}},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"hi-c","label":{"en":"Hi-C"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":null,"en":null}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"nextera-mate-pair-sample-preparation-kit","label":{"en":"Nextera Mate Pair Sample Preparation Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"超音波断片化（Covaris S2）","en":"Ultrasonic fragmentation (Covaris S2)"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq","label":{"en":"Illumina HiSeq"}}]},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":[{"code":"paired-end","label":{"ja":"ペアエンド","en":"Paired-end"}}]},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":[{"value":150,"unit":"bp","high":null}]},{"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":"BWA-mem","en":"BWA-mem"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"\"juicer\" software内で実施","en":"performed at \"juicer\" software"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"HiCCUPS","en":"HiCCUPS"}},{"key":"read-count","label":{"ja":"リード数","en":"Read count"},"type":"text","text":{"ja":"3億7千万- 4億","en":"370 million - 400 million"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":null},{"key":"coverage-breadth","label":{"ja":"カバレッジ (割合)","en":"Coverage (breadth)"},"type":"number","numbers":null},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"hi-c-loops","label":{"en":"Hi-C loops"}}]},{"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":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}