{"id":"E-GEAD-623","research":"hum0406","url":"https://humandbs.dbcls.jp/dataset/E-GEAD-623","datePublished":"2023-08-30","dateModified":"2023-08-30","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（RNA-seq）","en":"NGS (RNA-seq)"}}],"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":"SFTPCバリアントにおける家族性間質性肺炎（ICD10：J84.9）：1症例\n1: 患者血液から樹立したiPS細胞由来肺胞オルガノイドのEpCAM+CPM+細胞 ：3検体\n2: 患者血液から樹立したiPS細胞由来肺胞オルガノイドのEpCAM-CPM-細胞 ：3検体\n3: 患者血液から樹立した修復iPS細胞由来肺胞オルガノイドのEpCAM+CPM+細胞 ：3検体\n4: 患者血液から樹立した修復iPS細胞由来肺胞オルガノイドのEpCAM-CPM-細胞 ：3検体","en":"Familial interstitial pneumonia with SFTPC variant (ICD10: J84.9): 1 case\n- EpCAM+CPM+ or EpCAM-CPM- cells of alveolar organoids derived from iPSCs established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each\n- EpCAM+CPM+ or EpCAM-CPM- cells of Y104H-KO iPSC-derived alveolar organoids established from PBMCs of the patient with Y104H variant of SFTPC: 3 samples each"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"J849","label":{"ja":"間質性肺疾患，詳細不明","en":"Interstitial pulmonary disease, unspecified"}}],"name":{"ja":"SFTPCバリアントにおける家族性間質性肺炎","en":"Familial interstitial pneumonia with SFTPC variant"}}]},{"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":1,"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":"フローサイトメトリーにより分離した誘導型2型肺胞上皮（iAT2）細胞（EpCAM+CPM+）および線維芽細胞（EpCAM-CPM-）より抽出したRNA","en":"RNAs extracted from EpCAM+CPM+ or EpCAM-CPM- cells derived from iPSCs established from PBMCs of a patient with Y104H variant of SFTPC"}},{"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":"rna-seq","label":{"en":"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":"illumina-stranded-total-rna-prep-ligation-with-ribo-zero-plus","label":{"en":"Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"高温条件下での2価陽イオンによる断片化","en":"Exposure to divalent cations at elevated temperatures"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-nextseq-2000","label":{"en":"Illumina NextSeq 2000"}}]},{"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":59,"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 2.7.10b","en":"STAR 2.7.10b"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"RSeQC package","en":"RSeQC package"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"HTSeq package","en":"HTSeq package"}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":36602,"unit":null,"high":null,"suffix":{"ja":" 遺伝子","en":" genes"}}]},{"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":738280,"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"csv","label":{"en":"CSV"}}]}