{"id":"NHA000166","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000166","datePublished":"2022-02-08","dateModified":"2022-02-08","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":"eQTL解析データ","en":"eQTL data"}}],"experiments":[{"label":"eQTL","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"日本人集団：141名","en":"141 Japanese individuals"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":141,"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":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"JGAS000504のリードカウントデータおよび全血から抽出したgenomic DNAを用いた全ゲノムシーケンスデータ","en":"read count data of JGAS000504 and whole genome sequencing data using genomic DNA exracted 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":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"eqtl","label":{"en":"eQTL"}}]},{"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":"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-hiseq-x","label":{"en":"Illumina HiSeq X"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"リードカウントについてはJGAS000504を参照のこと\n全ゲノムシーケンスデータはGenotype call rate <90%, ExcessHet > 60, Hardy-Weinberg平衡検定P値<1.0×10−10のバリアントを除外した上で、Beagle v5.1によるgenotype imputationを実施した。","en":"See JGAS000504 for read count data.\nWGS: We removed the variants (i)with low genotyping call rates (<0.90), (ii)with ExcessHet > 60 or (iii) with Hardy-Weinberg Pvalue < 1.0 × 10−10. Genotype refinement was performed using Beagle v5.1."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"リードカウントについてはJGAS000504を参照のこと\n全ゲノムシーケンスデータはBWA-MEM v0.7.13を用いGRCh37にアラインメントし、GATK v3.8-0を用いbest practiceに準じて解析した。\nWe analyzed the association between genetic variants with minor allele frequency (MAF) ≥ 0.01 within a cis-window around each miRNA (±1 Mb of the mature miRNA) and normalized expression values using MatrixEQTL v2.3.","en":"See JGAS000504 for read count data.\nWGS: Sequenced reads were aligned against the reference human genome with the decoy sequence (GRCh37, human_g1k_v37_decoy) using BWA-MEM v0.7.13.\nWe analyzed the association between genetic variants with minor allele frequency (MAF) ≥ 0.01 within a cis-window around each miRNA (±1 Mb of the mature miRNA) and normalized expression values using MatrixEQTL v2.3."}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":12171854,"unit":null,"high":null,"prefix":{"ja":"全ゲノムシーケンスデータ: ","en":"Whole-genome sequencing data: "},"suffix":{"ja":" variants","en":" variants"}}]},{"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)"}}]}]}],"fileFormats":[{"code":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}