{"id":"JGAD000742","research":"hum0394","url":"https://humandbs.dbcls.jp/dataset/JGAD000742","datePublished":"2024-04-05","dateModified":"2024-04-05","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（Visium Spatial Gene Expression）、病理画像\nXenium In Situ Gene Expression\nMultiplex Fluorescence Immunostaining","en":"NGS (Visium Spatial Gene Expression), Histological image\nXenium In Situ Gene Expression\nMultiplex Fluorescence Immunostaining"}}],"experiments":[{"label":"Xenium 空間トランスクリプトーム","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"非小細胞肺がん（ICD10：C349）：5症例\n腫瘍組織：5検体","en":"non-small cell lung cancer (ICD10: C349): 5 cases\nsurgical section: 5 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C349","label":{"ja":"気管支又は肺，部位不明","en":"Malignant neoplasm: Bronchus or lung, unspecified"}}],"name":{"ja":"非小細胞肺がん","en":"non-small cell lung cancer"}}]},{"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":5,"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":"手術検体の腫瘍組織（凍結およびFFPE切片）","en":"surgical sections (fresh-frozen/FFPE)"}},{"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":"spatial-transcriptomics","label":{"en":"Spatial transcriptomics"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":"302遺伝子（Human Lung panel：202遺伝子、カスタム：100遺伝子）","en":"302 genes (Human Lung panel: 202 genes, custom: 100 genes)"}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"xenium-slides-sample-prep-reagents","label":{"en":"Xenium Slides & Sample Prep Reagents"}},{"code":"xenium-decoding-reagents","label":{"en":"Xenium Decoding Reagents"}},{"code":"xenium-decoding-consumables","label":{"en":"Xenium Decoding Consumables"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"10x-genomics-xenium-analyzer","label":{"en":"10x Genomics Xenium Analyzer"}}]},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"xenium-1.1.0.2、xenium-1.2.0.3","en":"xenium-1.1.0.2, xenium-1.2.0.3"}},{"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)"}}]}]},{"label":"Multiplex Fluorescence Immunostaining","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"非小細胞肺がん（ICD10：C349）：3症例\n腫瘍組織：3検体","en":"lung adenocarcinoma (ICD10: C349): 3 cases\ntumor tissues: 3 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C349","label":{"ja":"気管支又は肺，部位不明","en":"Malignant neoplasm: Bronchus or lung, unspecified"}}],"name":{"ja":"非小細胞肺がん","en":"lung adenocarcinoma"}}]},{"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":"肺腺がんの腫瘍組織","en":"tumor tissues of lung adenocarcinomas"}},{"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":"multiplex-fluorescence-immunostaining","label":{"en":"Multiplex fluorescence immunostaining"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":"Cycle/蛍光タンパク質対応表","en":"cycle/probe information"}},{"key":"sample-processing","label":{"ja":"試料の処理","en":"Sample processing"},"type":"text","text":{"ja":"細胞処理: Staining Kit for PhenoCycler","en":"Cell treatment: Staining Kit for PhenoCycler"}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"staining-kit-for-phenocycler","label":{"en":"Staining Kit for PhenoCycler"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"akoya-biosciences-phenocycler","label":{"en":"Akoya Biosciences PhenoCycler"}}]},{"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)"}}]}]},{"label":"Visium 空間トランスクリプトーム + 病理画像","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"非小細胞肺がん（ICD10：C349）：8症例\n腫瘍組織：16検体","en":"non-small cell lung cancer (ICD10: C349): 8 cases\nsurgical section: 16 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C349","label":{"ja":"気管支又は肺，部位不明","en":"Malignant neoplasm: Bronchus or lung, unspecified"}}],"name":{"ja":"非小細胞肺がん","en":"non-small cell lung cancer"}}]},{"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":8,"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":"手術検体の凍結切片におけるRNA、および、FFPE切片においてRNAとハイブリダイズしたプローブ","en":"RNAs extracted from surgical sections (fresh-frozen/FFPE)"}},{"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":"spatial-transcriptomics","label":{"en":"Spatial transcriptomics"}},{"code":"histological-image","label":{"en":"Histological image"}}]},{"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":"visium-spatial-gene-expression","label":{"en":"Visium Spatial Gene Expression"}}]},{"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-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}}]},{"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":118,"unit":"bp","high":null,"prefix":{"ja":"新鮮凍結: ","en":"fresh-frozen: "}},{"value":78,"unit":"bp","high":null,"prefix":{"ja":"FFPE: ","en":"FFPE: "}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":null,"en":null}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"spaceranger-1.2.1、spaceranger-1.3.0","en":"spaceranger-1.2.1, spaceranger-1.3.0"}},{"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":502509542962,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"tsv","label":{"en":"TSV"}},{"code":"csv","label":{"en":"CSV"}},{"code":"xlsx","label":{"en":"XLSX"}},{"code":"json","label":{"en":"JSON"}},{"code":"mtx","label":{"en":"MTX"}},{"code":"cloupe","label":{"en":"CLOUPE"}},{"code":"html","label":{"en":"HTML"}},{"code":"png","label":{"en":"PNG"}},{"code":"qptiff","label":{"en":"QPTIFF"}},{"code":"tar","label":{"en":"TAR"}}]}