{"id":"JGAD000371","research":"hum0214","url":"https://humandbs.dbcls.jp/dataset/JGAD000371","datePublished":"2022-03-16","dateModified":"2022-03-16","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：全身性強皮症）","en":"NGS (RNA-seq: Systemic sclerosis)"}}],"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":"全身性エリテマトーデス（ICD10：M329）：107症例\n対照健常者：92名","en":"Systemic Lupus Erythematosus (ICD10: M329): 107 cases\n92 healthy controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"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"}}]},{"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":199,"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":"末梢血免疫細胞19画分（Naive_CD4, Mem_CD4, Fr._II_eTreg, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CD16n_Mono, CD16p_Mono, mDC, pDC）より抽出したtotal RNA","en":"Total RNAs extracted from 19 immune cell subsets (Naive_CD4, Mem_CD4, Fr._II_eTreg, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CD16n_Mono, CD16p_Mono, mDC, pDC)"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"immune-cell","label":{"en":"Immune 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-seq2","label":{"en":"Smart-seq2"}},{"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 v2（test cohort）、SMART-seq v4 Ultra Low Input RNA Kit（validation cohort）","en":"Smart-Seq v2 for the test cohort and SMART-seq v4 Ultra Low Input RNA Kit for the validation cohort"}},{"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":76,"unit":"bp","high":null,"suffix":{"ja":" (テストコホート)","en":" (test cohort)"}},{"value":100,"unit":"bp","high":null,"suffix":{"ja":" (検証コホート)","en":" (validation cohort)"}}]},{"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":"FASTQファイルはSTAR（v2.5）によってGRCh38; GenBank assembly GCA_000001405.18にマッピングした。カウントテーブルの作成にはHTSeq-count（v0.6.1）を用いた。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）。ミトコンドリア遺伝子発現は細胞ストレスを反映するため、ミトコンドリア遺伝子発現 <8%をカットオフに追加した。同一サブセット内の遺伝子発現の相関係数（r）を計算し、r2 < 0.8のサンプルは外れ値として除外した。","en":"FASTQ files were aligned to the human genome (GRCh38; GenBank assembly GCA_000001405.18) using STAR (v2.5). HTSeq-count (v0.6.1) was used to generate gene counts. In the quality-control analysis, low-quality bases (Phred quality score < 20) were trimmed using the fastx-toolkit (v0.0.14). As the level of mitochondrial transcription is an indicator of cell stress, we applied a cutoff percentage of mitochondrial gene transcripts of < 8%. For detecting outlier samples, Spearman's correlation for each subset was calculated, and samples with an average r2 < 0.8 were omitted as outliers."}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":26354,"unit":null,"high":null,"suffix":{"ja":" (テストコホート)","en":" (test cohort)"}},{"value":26485,"unit":null,"high":null,"suffix":{"ja":" (検証コホート)","en":" (validation cohort)"}}]},{"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":[]}