{"id":"E-GEAD-1308","research":"hum0600","url":"https://humandbs.dbcls.jp/dataset/E-GEAD-1308","datePublished":"2026-09-07","dateModified":"2026-09-07","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":"scRNA-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"甲状腺未分化がん（ICD10：C73）：3症例\n腫瘍組織：3検体\n甲状腺乳頭がん（ICD10：C73）：3症例\n腫瘍組織：3検体","en":"undifferentiated thyroid carcinoma (ICD10: C73): 3 cases\ntumor tissue: 3 samples\npapillary thyroid carcinoma (ICD10: C73): 3 cases\ntumor tissue: 3 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C73","label":{"ja":"甲状腺の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of thyroid gland"}}],"name":{"ja":"甲状腺未分化がん","en":"undifferentiated thyroid carcinoma"}},{"terms":[{"code":"C73","label":{"ja":"甲状腺の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of thyroid gland"}}],"name":{"ja":"甲状腺乳頭がん","en":"papillary thyroid carcinoma"}}]},{"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":6,"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":"腫瘍組織より単離した細胞から抽出したRNA","en":"RNA extracted from a single cell isolated from tumor tissues"}},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"tumor","label":{"ja":"腫瘍","en":"Tumor"}}]},{"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":"chromium-next-gem-single-cell-3-v3-1","label":{"en":"Chromium Next GEM Single Cell 3' v3.1"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"酵素反応","en":"Enzymatic fragmentation"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}}]},{"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":90,"unit":"bp","high":null}]},{"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","en":"STAR"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"RのSeuratパッケージを用い、各サンプルに対して以下の基準で低クオリティ細胞およびダブレットを除外した\n- 検出遺伝子数（nFeature_RNA）：各サンプルの検出遺伝子数分布において、上下各0.5% tailの細胞を除外\n- ミトコンドリア遺伝子比率（percent.mt）：ミトコンドリア由来の転写産物割合が 80%以上（percent.mt ≥ 80%）の死細胞を除外\n- ダブレット除去：ソフトウェア DoubletFinder (version 2.0.6) を使用し、2個以上の細胞が1つの液滴に入ってしまった擬陽性データを除外","en":"Using the Seurat package in R, low-quality cells were removed by discarding the bottom and top 0.5% tails of the nFeature_RNA distribution per sample and cells with high mitochondrial content (percent.mt ≥ 80%). Doublets were identified with DoubletFinder (version 2.0.6)."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Cell Ranger (v7.1.0)","en":"Cell Ranger (v7.1.0)"}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":30000,"unit":null,"high":40000,"suffix":{"ja":" genes (約)","en":" genes (Approx.)"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"gene-expression-matrix","label":{"ja":"遺伝子発現行列","en":"Gene expression matrix"}}]},{"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":233664275,"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"hdf5","label":{"en":"HDF5"}}]}