{"id":"E-GEAD-397","research":"hum0214","url":"https://humandbs.dbcls.jp/dataset/E-GEAD-397","datePublished":"2021-04-30","dateModified":"2021-05-13","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":"RNA-seqのリードカウント","en":"Read count data from 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）：62症例\n筋炎（ICD10：M339、M332）：65症例\n全身性強皮症（ICD10：M340）：67症例\n混合性結合組織病（ICD10：M351）：19症例\nシェーグレン症候群（ICD10：M350）：18症例\n関節リウマチ（ICD10：M0690）：25症例\nベーチェット病（ICD10：M352）：23症例\n成人スチル病（ICD10：M0610）：18症例\nANCA関連血管炎（ICD10：M318）：26症例\n高安動脈炎（ICD10：M314）：16症例\n対照健常者：92名","en":"Systemic Lupus Erythematosus (ICD10: M329): 62 cases\nMyositis (ICD10: M339, M332): 65 cases\nSystemic Sclerosis (ICD10: M340): 67 cases\nMixed Connective Tissue Disease (ICD10: M351): 19 cases\nSjögren's Syndrome (ICD10: M350): 18 cases\nRheumatoid Arthritis (ICD10: M0690): 25 cases\nBehçet's Disease (ICD10: M352): 23 cases\nAdult Onset Still's Disease (ICD10: M0610): 18 cases\nANCA-associated Vasculitis (ICD10: M318: 26 cases\nTakayasu's Arteritis (ICD10: M314): 16 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"}},{"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":"筋炎","en":"Myositis"}},{"terms":[{"code":"M340","label":{"ja":"全身性進行性硬化症","en":"Progressive systemic sclerosis"}}],"name":{"ja":"全身性強皮症","en":"Systemic Sclerosis"}},{"terms":[{"code":"M351","label":{"ja":"その他の重複症候群","en":"Other overlap syndromes"}}],"name":{"ja":"混合性結合組織病","en":"Mixed Connective Tissue Disease"}},{"terms":[{"code":"M350","label":{"ja":"乾燥症候群［シェーグレン＜Sjogren＞症候群］","en":"Sicca syndrome [Sjögren]"}}],"name":{"ja":"シェーグレン症候群","en":"Sjögren's Syndrome"}},{"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":"M352","label":{"ja":"ベーチェット＜Behcet＞病","en":"Behçet disease"}}],"name":{"ja":"ベーチェット病","en":"Behçet's Disease"}},{"terms":[{"code":"M061","label":{"ja":"成人発症スチル＜Still＞病","en":"Adult-onset Still disease"}}],"name":{"ja":"成人スチル病","en":"Adult Onset Still's Disease"}},{"terms":[{"code":"M318","label":{"ja":"その他の明示されたえ＜壊＞死性血管障害","en":"Other specified necrotizing vasculopathies"}}],"name":{"ja":"ANCA関連血管炎","en":"ANCA-associated Vasculitis"}},{"terms":[{"code":"M314","label":{"ja":"大動脈弓症候群［高安病］","en":"Aortic arch syndrome [Takayasu]"}}],"name":{"ja":"高安動脈炎","en":"Takayasu's Arteritis"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":431,"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28画分（Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono（別名CD16n_Mono）, CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu）より抽出したtotal RNA","en":"Total RNAs extracted from 28 immune cell subsets (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu)"}},{"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":"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":"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。解析に不適切なサンプルの除外基準としては、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":53344,"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":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"included","label":{"ja":"あり","en":"Included"}}]},{"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":286026625,"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"tar","label":{"en":"TAR"}}]}