{"id":"NHA000172","research":"hum0343","url":"https://humandbs.dbcls.jp/dataset/NHA000172","datePublished":"2022-06-14","dateModified":"2022-06-14","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":"COVID19感染者末梢血のRNA-seq解析データ・SNPアレイデータより算出したeQTL/sQTLサマリーデータ","en":"eQTL/sQTL summary statistics for COVID-19"}}],"experiments":[{"label":"eQTL/sQTL summary statistics","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"COVID-19感染者（ICD-10：U071）：465症例 （重症者 359名、軽症者 106名）","en":"COVID-19 (ICD-10: U071): 465 cases (severe cases: 359, mild case: 106)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"U071","label":{"ja":"コロナウイルス感染症2019，ウイルスが同定されたもの","en":"COVID-19, virus identified"}}],"name":{"ja":"COVID-19感染者","en":"COVID-19"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"affected","label":{"ja":"罹患","en":"Affected"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":465,"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":"RNA-seqで得られたfastqデータ、およびGWASで用いられたSNPアレイデータ","en":"read count data of RNA-seq and SNP array data of GWAS"}},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"eqtl","label":{"en":"eQTL"}},{"code":"sqtl","label":{"en":"sQTL"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}},{"code":"illumina-infinium-asian-screening-array","label":{"en":"Illumina Infinium Asian Screening Array"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"GTEx パイプライン （https://github.com/broadinstitute/gtex-pipeline/）に準拠","en":"Following GTEx pipeline (https://github.com/broadinstitute/gtex-pipeline/)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Gene level quantification and normalization： RSEM (v1.3.3)\nIntron cluster quantification： LeafCutter（ v0.2.7）\n各遺伝子転写開始点に関して、+-1Mb以内に存在する（= cis）変異（頻度>1%）のeQTL効果をfastQTLを用い検定した。\np値が0.05以下である変異-遺伝子組の、変異頻度、p値、効果量、原因変異確率の推定値（=PIP）をsummary dataとした。\n各遺伝子転写開始点に関してtrans-eQTL効果はtensorQTLを用い検定した。\np値が5.0*10^8以下である変異-遺伝子組の、変異頻度、p値、効果量をsummary dataとした。\n各イントロン分岐点に関して、+-1Mb以内に存在する変異（頻度>1%）のsQTL効果をfastQTLを用い検定した。\np値が0.05以下である変異-イントロン領域組の、変異頻度、p値、効果量、PIPをsummary dataとした。","en":"Gene level quantification and normalization: RSEM (v1.3.3)\nIntron cluster quantification: LeafCutter (v0.2.7)\nThe eQTL effects of common (>1%) variants in cis (<+-1Mb) window of transcription sites were tested using fastQTL. Variant-gene pairs with cis-eQTL p-value<0.05, annotated with allele frequency (AF), p-value, effect size (beta) and posterior inclusion probability (PIP) were summarized.\nTrans-eQTL effects were tested using tensorQTL. Variant-gene pairs with trans-eQTL p-value <5*10^-8, annotated with AF, p-value and beta were summarized.\nThe sQTL effects of common (>1%) variants in cis (<+-1Mb) window of intron cluster start sites were tested using fastQTL. Variant-intron cluster pairs with cis-sQTL p-value<0.05, annotated with AF, p-value, beta and PIP were summarized."}},{"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"}},{"code":"sqtl-summary-statistics","label":{"en":"sQTL 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":"txt","label":{"en":"TXT"}},{"code":"zip","label":{"en":"ZIP"}}]}