{"id":"E-GEAD-344","research":"hum0218","url":"https://humandbs.dbcls.jp/dataset/E-GEAD-344","datePublished":"2020-10-10","dateModified":"2020-10-10","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":"NGS（scRNA-seq）","en":"NGS (scRNA-seq)"}}],"experiments":[{"label":{"ja":"scRNA-seq","en":"scRNA-seq"},"values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"抗Sc1-70抗体陽性全身性強皮症（ICD10：M340）：3症例","en":"Systemic sclerosis (ICD10: M340): 3 cases"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"M340","label":{"ja":"全身性進行性硬化症","en":"Progressive systemic sclerosis"}}],"name":{"ja":"抗Sc1-70抗体陽性全身性強皮症","en":"Systemic sclerosis"}}]},{"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":3,"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":"末梢血より単球を分取し、単細胞へ分離した上で抽出したmRNA","en":"RNAs extracted from a single cell isolated from peripheral blood monocytes"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"monocyte","label":{"ja":"単球","en":"Monocyte"}}]},{"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":"scrna-seq","label":{"en":"scRNA-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-icell8-3-de-reagent-kit","label":{"en":"SMARTer ICELL8 3' DE Reagent Kit"}},{"code":"nextera-xt-dna-library-prep-kit","label":{"en":"Nextera XT DNA Library Prep Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"Nextera XT DNA Library Prep Kit","en":"Nextera XT DNA Library Prep Kit"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq","label":{"en":"Illumina HiSeq"}}]},{"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":25,"unit":"bp","high":null,"prefix":{"ja":"Read1: ","en":"Read1: "}},{"value":100,"unit":"bp","high":null,"prefix":{"ja":"Read2: ","en":"Read2: "}}]},{"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":"STAR（GRCh38）","en":"STAR (GRCh38)"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"プライマー、ポリA,ポリT、 low-quality ends（phred quality score < 25）はCutadaptでトリムした。トリム後にリード長 < 20 塩基のリードを除去した。","en":"The sequencing primer, poly-A, and poly-T were trimmed by Cutadapt and low-quality ends (phred quality score < 25) were also trimmed. After trimming, the read (the length of which was < 20 bases) was also removed."}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":26288,"unit":null,"high":null}]},{"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":1485749,"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"tsv","label":{"en":"TSV"}}]}