{"id":"E-GEAD-398","research":"hum0214","url":"https://humandbs.dbcls.jp/dataset/E-GEAD-398","datePublished":"2021-04-30","dateModified":"2021-04-30","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":"Conditional eQTLサマリーデータ（有意データのみ）","en":"Conditional eQTL summary data (significant associations)"}}],"experiments":[{"label":{"ja":"Single-cell eQTL (scRNA-seq + WGS)","en":"Single-cell eQTL (scRNA-seq + WGS)"},"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）：24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）：25症例\n高安動脈炎（ICD10：M314）：16症例\n対照健常者：79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): 24 cases\nBehçet's Disease (ICD10: M352): 23 cases\nAdult Onset Still's Disease (ICD10: M0610): 18 cases\nANCA-associated Vasculitis (ICD10: M318: 25 cases\nTakayasu's Arteritis (ICD10: M314): 16 cases\n79 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":416,"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":"全血より抽出したDNA","en":"DNAs extracted from whole blood"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}}]},{"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":"eqtl","label":{"en":"eQTL"}}]},{"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":"truseq-dna-pcr-free-library-prep-kit","label":{"en":"TruSeq DNA PCR-Free Library Prep Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"TruSeq DNA PCR-Free Library prep kit","en":"TruSeq DNA PCR-Free Library prep kit"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}}]},{"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":151,"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":"BWA-MEM（GRCh38）","en":"BWA-MEM(GRCh38)"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"全ゲノムシーケンスデータはGATK（v 4.0.6.0）best practiceに準じて解析した。検出バリアント率が99%未満のサンプルは除外した。遺伝型のインピュテーションにはBEAGLE（v 5.1）を用いた。Call rate <85%, Hardy-Weinberg平衡検定P値<1.0x10-6, マイナーアレル頻度1%未満のバリアントは除外した。","en":"WGS data processing was performed based on the standardized best-practice method proposed by GATK (v 4.0.6.0). Samples with genotyping call rates < 99% were removed. We used BEAGLE (v 5.1) to impute missing genotypes. Variants with call rate < 85%, HWE P-value < 1.0 x 10-6 or minor allele frequency < 1% were excluded."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"各細胞サブセットで80%を超えるサンプルで5リード未満、もしくは0.5 CPM未満の低発現遺伝子を除外した。常染色体遺伝子発現データのTMMノーマライゼーション、CPM変換、inverse normal transformによるサンプル間ノーマライゼーションを実施した。また隠れた共変量の推測のためPEERを実施した。eQTL解析の共変量として、上位2つの遺伝子主成分、サンプル回収のphase、性別、PEERによる潜在的因子を含めた。Phase 1で回収したMem CD8はPhase 2ではCM CD8とEM CD8として分割しているため、大部分の細胞の含まれるEM CD8と統合してeQTL解析を実施した。各細胞サブセットでのConditional eQTL解析では、QTLtoolsのpermutation passによる10000回のパーミュテーションを実施し、各遺伝子レベルでのFDR <0.05と対応するnominal p-value thresholdを定めた。その上で、QTL toolsのconditional passを用いてforward-backward stepwise regression eQTL analysisを実施した。Nominal eQTL解析では QTL toolsのnominal passを用いて、各遺伝子の転写開始点から1M塩基対のバリアントと遺伝子発現の関連を解析した。","en":"Genes expressed at low levels (< 5 count in more than 80% samples or < 0.5 CPM in more than 80% samples) were filtered out in each cell subset. The residual autosomal expression data were normalized between samples with TMM, converted to CPM and then normalized across samples using an inverse normal transform. A Probabilistic Estimation of Expression Residuals (PEER) method was applied to normalized expression data to infer hidden covariates. The top 2 genetic principal components, sample collection phase, clinical diagnosis, sex and latent factors were utilized as covariates for eQTL analysis. Mem CD8s, which were collected in Phase1 and divided into CM CD8 and EM CD8 in Phase2, were analyzed jointly with EM CD8 for eQTL analysis because the majority of the Mem CD8 population consisted of EM CD8. For each cell subset conditional eQTL analysis, we used a QTLtools permutation pass with 10,000 permutations to obtain gene-level nominal P value thresholds corresponding to FDR < 0.05. We subsequently performed forward-backward stepwise regression eQTL analysis with a QTLtools conditional pass. For nominal eQTL analysis, we used a QTLtools nominal pass and tested for the association of the variants located within 1Mbp from the TSS of the genes."}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":19441,"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":"eqtl-summary-statistics","label":{"ja":"eQTL 要約統計量","en":"eQTL summary statistics"}}]},{"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":564882923,"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"tar","label":{"en":"TAR"}}]}