{"id":"NHA000132","research":"hum0207","url":"https://humandbs.dbcls.jp/dataset/NHA000132","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（ChIP-seq）によるエンリッチ領域ピーク情報","en":"Peaks from NGS (ChIP-seq)"}}],"experiments":[{"label":"ChIP-seq","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）：20症例\n変形性関節症（ICD10：M06）：20症例\n1症例あたり、末梢血リンパ球 5分画（CD4陽性T細胞, CD8陽性T細胞, B細胞, NK細胞, 単球）と滑膜線維芽細胞 10条件（無刺激, TNF-α, IL-1β, IL-6/sIL-6R, IL-17A, IL-18, IFN-γ, IFN-α, TGF-β1, 8-mix）を用意し、同じ条件のサンプルを疾患群ごとにプール後、3種の抗体（H3K4me1, H3K4me3, H3K27ac）を用いた免疫沈降を実施：計90検体中、quality control条件をパスした83検体","en":"rheumatoid arthritis (ICD10: M05): 20 cases\nosteoarthritis (ICD10: M06): 20 cases\n5 fractions of PBMCs (CD4+ T, CD8+ T, B, NK and monocytes) and 10 conditions of synovial fibroblasts (unstimulated, IFN-α, IFN-γ, TNF-α, IL-1β, IL-6/sIL-6R, IL-17, TGF-β1, IL-18 and 8-mix) were prepared for 1 case each. Samples under the same condition were pooled and immunoprecipitated with 3 anti-histone antibodies (H3K4me1, H3K4me3, H3K27ac): total 83 samples (7 samples were excluded because of QC)"}},{"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"}},{"terms":[{"code":"M06","label":{"ja":"その他の関節リウマチ","en":"Other rheumatoid arthritis"}}],"name":{"ja":"変形性関節症","en":"osteoarthritis"}}]},{"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":40,"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・変形性関節症患者由来の各細胞に対して免疫沈降実施後抽出したDNA","en":"DNAs were extracted from cells from rheumatoid arthritis and osteoarthritis patients. Then, samples under the same condition were pooled and immunoprecipitated with anti-histone antibodies."}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"cd4-t-cell","label":{"ja":"CD4 陽性 T 細胞","en":"CD4+ T cell"}},{"code":"cd8-t-cell","label":{"ja":"CD8 陽性 T 細胞","en":"CD8+ T cell"}},{"code":"b-cell","label":{"ja":"B 細胞","en":"B cell"}},{"code":"nk-cell","label":{"ja":"NK 細胞","en":"NK cell"}},{"code":"monocyte","label":{"ja":"単球","en":"Monocyte"}},{"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":"chip-seq","label":{"en":"ChIP-seq"}}]},{"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":"chip-it-high-sensitivity-kit","label":{"en":"ChIP-IT High Sensitivity Kit"}},{"code":"chip-it-pbmc-kit","label":{"en":"ChIP-IT PBMC 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-2500","label":{"en":"Illumina HiSeq 2500"}}]},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":[{"code":"single-end","label":{"ja":"シングルエンド","en":"Single-end"}}]},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":[{"value":50,"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":"Bowtie2","en":"Bowtie2"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"アダプタートリミング cutadapt、クオリティトリミング fastxtoolkit（クオリティスコア < 20の塩基を除去、塩基数 < 50 のリードを除去、クオリティスコア < 20の塩基が20%より多いリードを除去）","en":"adapter trimming: cutadapt, quality trimming: fastxtoolkit (bases with quality score < 20 were excluded, reads with base number < 50 were excluded, reads including 20% or more of bases with quality score < 20 were excluded)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"MACS 2.0","en":"MACS 2.0"}},{"key":"read-count","label":{"ja":"リード数","en":"Read count"},"type":"text","text":{"ja":"2000万-5000万 / -","en":"20-50 million\n-"}},{"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":"peak-calls","label":{"en":"Peak calls"}}]},{"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"}}]}