{"id":"JGAD000756","research":"hum0214","url":"https://humandbs.dbcls.jp/dataset/JGAD000756","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":"全身性エリテマトーデス（ICD10：M329）：136症例\n対照健常者：89名","en":"Systemic Lupus Erythematosus (ICD10: M329): 136 cases\n89 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":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血免疫細胞27画分（Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA, Naive_CD8, Naive_B, SM_B, USM_B, DN_B, Plasmablast, NK, CD16p_Mono, CL_Mono, Neu, mDC, pDC, TEMRA_CD8, CM_CD8, EM_CD8, NC_Mono, Int_Mono, LDG）より抽出したtotal RNA","en":"Total RNAs extracted from 27 immune cell subsets (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA, Naive_CD8, Naive_B, SM_B, USM_B, DN_B, Plasmablast, NK, CD16p_Mono, CL_Mono, Neu, mDC, pDC, TEMRA_CD8, CM_CD8, EM_CD8, NC_Mono, Int_Mono, LDG)"}},{"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"}},{"code":"illumina-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}}]},{"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,"suffix":{"ja":" (HiSeq 2500)","en":" (HiSeq 2500)"}},{"value":150,"unit":"bp","high":null,"suffix":{"ja":" (NovaSeq 6000)","en":" (NovaSeq 6000)"}}]},{"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":"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。ユニークマップ率が80%未満、もしくはユニークマップリード数が5.00 x 10⁶未満のサンプルは除去した。同一サブセット内の遺伝子発現の相関係数（Di）が0.9未満のサンプルは除去した。同一個人のwhole genome sequencingのhetero locusに対するgenotypeの一致率が0.9未満のサンプルは除去した。","en":"Adaptor sequences were trimmed using Cutadapt and reads containing low-quality bases (Phred quality score < 20 in > 20% of the bases) were removed. Reads were aligned to the human genome within the UCSC Genome Browser (GRCh38) using STAR, and expression was counted with HTSeq. Samples with uniquely mapped read rates < 80% or unique read counts < 5 × 10⁶ were excluded. We calculated Spearman's correlations of the expressions between two samples from the same cell type and then removed the samples with mean correlation coefficients < 0.9. In addition, samples with the concordance rates between RNA-seq-based genotype and WGS-based genotype at the heterozygous loci < 0.9 were excluded."}},{"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":129437621,"fileFormats":[{"code":"txt","label":{"en":"TXT"}}]}