{"id":"JGAD000755","research":"hum0214","url":"https://humandbs.dbcls.jp/dataset/JGAD000755","datePublished":"2024-02-14","dateModified":"2024-02-14","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"NGS（RNA-seq）解析によるリードカウントデータ","en":"NGS (RNA-seq)"}}],"experiments":[{"label":{"ja":"RNA-seq","en":"RNA-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：M0690）：19症例\n全身性エリテマトーデス（ICD10：M329）：62症例\n特発性炎症性筋疾患（ICD10：M339、M332）：40症例\n対照健常者：64名","en":"Rheumatoid Arthritis (ICD10: M0690): 19 cases\nSystemic Lupus Erythematosus (ICD10: M329): 62 cases\nIdiopathic Inflammatory Myopathy (ICD10: M339, M332): 40 cases\n64 healthy controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"M069","label":{"ja":"関節リウマチ，詳細不明","en":"Rheumatoid arthritis, unspecified"}}],"name":{"ja":"関節リウマチ","en":"Rheumatoid Arthritis"}},{"terms":[{"code":"M329","label":{"ja":"全身性エリテマトーデス＜紅斑性狼瘡＞＜SLE＞，詳細不明","en":"Systemic lupus erythematosus, unspecified"}}],"name":{"ja":"全身性エリテマトーデス","en":"Systemic Lupus Erythematosus"}},{"terms":[{"code":"M339","label":{"ja":"皮膚（多発性）筋炎，詳細不明","en":"Dermatopolymyositis, unspecified"}},{"code":"M332","label":{"ja":"多発性筋炎","en":"Polymyositis"}}],"name":{"ja":"特発性炎症性筋疾患","en":"Idiopathic Inflammatory Myopathy"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血免疫細胞9画分（Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA）より抽出したtotal RNA","en":"Total RNAs extracted from 9 immune cell subsets (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA)"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"cd4-t-cell","label":{"ja":"CD4 陽性 T 細胞","en":"CD4+ T cell"}},{"code":"treg-cell","label":{"en":"Treg cell"}},{"code":"t-cell","label":{"ja":"T 細胞","en":"T cell"}}]},{"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":"rna-seq","label":{"en":"RNA-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":"smart-seq-v4-ultra-low-input-rna-kit","label":{"en":"SMART-Seq v4 Ultra Low Input RNA Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"SMART-seq v4 Ultra Low Input RNA Kit","en":"SMART-seq v4 Ultra Low Input RNA Kit"}},{"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":"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":100,"unit":"bp","high":null}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch38","label":{"en":"GRCh38"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"STAR（GRCh38）","en":"STAR (GRCh38)"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"cutadapt (v1.16)およびfastx-toolkit（v0.0.14）を用いてアダプター配列及び3'の低クオリティー塩基をトリムした（Phred quality score < 20）。低クオリティーの塩基が20%を超えるリードを除去した。STAR（v2.5.3）のtwo-pass modeを用いてGRCh38へのマッピングを行った（Gencode version 27アノテーション）。ユニークマップ率が90%未満（Plasmablastでは70%未満、他のB細胞サブセットでは<85%未満）、もしくはユニークマップリード数が6.00 x 10^6未満のサンプルは除去した。遺伝子発現はHTSeq（v 0.11.2）で定量した。各細胞分画で低発現遺伝子（90%を超えるサンプルで10リード未満）を除外し、edgeRのTMMノーマライゼーションを実施、ログcount per million（CPM）変換、ComBatによるバッチ除去を行った上で、同一サブセット内の遺伝子発現のSpearman相関係数を計算し、平均値が0.9未満のサンプルを除外した。","en":"From sequenced reads, adaptor sequences were trimmed using cutadapt (v1.16). In addition, 3′- ends with low-quality bases (Phred quality score < 20) were trimmed using the fastx-toolkit (v0.0.14). Reads containing more than 20% low-quality bases were removed. Subsequently, reads were aligned against the GRCh38 reference sequence using STAR (v2.5.3) in two-pass mode with Gencode version 27 annotations. We excluded samples with uniquely mapped read rates < 90% (with the exception of < 70% for plasmablasts and <85% for the other B cell subsets) or unique read counts < 6 × 10^6. Expression was quantified using HTSeq (v 0.11.2.). For QC of the expression data, in each cell population, we filtered low count genes (< 10 in > 90% of samples), normalized between samples with a trimmed mean of M values (TMM) implemented in edgeR software, converted to log-transformed count per million (CPM), removed batch effects using ComBat software and computed inter-sample Spearman's correlations of expression levels between each sample and the remaining samples from the same cell subset. We excluded samples with mean correlation coefficients less than 0.9."}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":26353,"unit":null,"high":null}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"count-data","label":{"ja":"カウントデータ","en":"Count 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)"}}]}]}],"dataVolume":36332844,"fileFormats":[{"code":"txt","label":{"en":"TXT"}}]}