{"id":"JGAD000621","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/JGAD000621","datePublished":"2022-02-21","dateModified":"2025-10-29","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":"miRNAリードカウント","en":"Read count data of miRNA"}}],"experiments":[{"label":"miRNA-seq","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":"末梢血単核細胞から抽出したRNA","en":"RNAs extracted from PBMC"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"pbmc","label":{"ja":"末梢血単核球 (PBMC)","en":"PBMC"}}]},{"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":"small-rna-seq","label":{"en":"Small 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":"smarter-smrna-seq-kit-for-illumina","label":{"en":"SMARTer smRNA-Seq Kit for Illumina"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":null,"en":null}},{"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":"single-end","label":{"ja":"シングルエンド","en":"Single-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":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"bowtie（GRCh37）","en":"bowtie (GRCh37)"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"We performed adapter trimming using Cutadapt v1.8 and removed reads with a low quality score (Phred quality score < 20 in >20% of total bases) using fastp v0.20.0. Also, we removed reads with a length of >29 bp or <15 bp, which are not expected to be mature miRNAs. Mature miRNAs detected with ≥1 read in at least half of the individuals were included in the dataset.","en":"We performed adapter trimming using Cutadapt v1.8 and removed reads with a low quality score (Phred quality score < 20 in >20% of total bases) using fastp v0.20.0. Also, we removed reads with a length of >29 bp or <15 bp, which are not expected to be mature miRNAs. Mature miRNAs detected with ≥1 read in at least half of the individuals were included in the dataset."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"featureCounts + miRbase v22","en":"featureCounts + miRbase v22"}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":343,"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":"mirna-expression-count","label":{"en":"miRNA expression count"}}]},{"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":54684,"fileFormats":[{"code":"tsv","label":{"en":"TSV"}}]}