{"id":"JGAD000059","research":"hum0055","url":"https://humandbs.dbcls.jp/dataset/JGAD000059","datePublished":"2020-09-28","dateModified":"2024-01-19","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）\nメチル化アレイ","en":"NGS (RNA-seq)\nMethylation array"}}],"experiments":[{"label":"RNA-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"NAFLD患者由来の肝臓組織：60検体","en":"Human liver tissues from NAFLD patients: 60 samples"}},{"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 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SNPs\ncross-reactive"}},{"key":"normalization","label":{"ja":"正規化","en":"Normalization"},"type":"text","text":{"ja":"DNAメチル化の生データはインターナル・コントロールのプローブで補正。\n2つのタイププローブについてはbeta-mixture quantile normalizationにて補正。\nバッチエフェクトはComBat（R/Bioconductor package ChAM）にて補正。","en":"Raw DNA methylation data were preprocessed by normalizing to appropriate internal control probes. The effects of two types of CpG probes on CpG methylation measurements were corrected using beta-mixture quantile normalization, and batch effects were corrected using a ComBat normalization method in the R/Bioconductor package ChAMP."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenomeStudio Software （Illumina）","en":"GenomeStudio Software (Illumina)"}},{"key":"probe-number","label":{"ja":"プローブ数","en":"Probe count"},"type":"number","numbers":[{"value":431736,"unit":null,"high":null,"suffix":{"ja":" (CpGs 常染色体上)","en":" (CpGs on autosomes)"}}]},{"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":330195178656,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"txt","label":{"en":"TXT"}}]}