{"id":"JGAD000861","research":"hum0469","url":"https://humandbs.dbcls.jp/dataset/JGAD000861","datePublished":"2024-08-19","dateModified":"2024-08-19","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（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":"妊娠初期スクリーニング検査を受けた妊婦（ICD10: O35.3）から採取した末梢血単核球：10名15検体\n12週と20週ごろのペア：1名（2検体）\n12週と36週ごろのペア：1名（2検体）\n20週と36週ごろのペア：2名（4検体）\n20週と28週ごろのペア：1名（2検体）\n12週ごろ：2名（2検体）\n20週ごろ：3名（3検体）","en":"Pregnant women undergoing early pregnancy screening (ICD10: O35.3): 10 cases 15 samples\na pair at 12 weeks and 20 weeks: 1 case\na pair at 12 weeks and 36 weeks: 1 case\na pair at 20 weeks and 36 weeks: 2 cases\na pair at 20 weeks and 28 weeks: 1 case\n2 specimens around 12 weeks\n3 specimens around 20 weeks"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"O353","label":{"ja":"母体のウイルス性疾患による胎児傷害（の疑い）のための母体ケア","en":"Maternal care for (suspected) damage to fetus from viral disease in mother"}}],"name":{"ja":"妊娠初期スクリーニング検査を受けた妊婦","en":"Pregnant women undergoing early pregnancy screening"}}]},{"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":10,"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":"sex","label":{"ja":"性別","en":"Sex"},"type":"vocabulary","terms":[{"code":"female","label":{"ja":"女性","en":"Female"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"PBMCから単離した抗原特異的T細胞より抽出したRNA","en":"RNAs extracted from CD8+ T cells"}},{"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":"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-chip-g-single-cell-kit","label":{"en":"Chromium Next GEM Chip G Single Cell Kit"}},{"code":"chromium-next-gem-single-cell-5-v2","label":{"en":"Chromium Next GEM Single Cell 5' v2"}},{"code":"chromium-single-cell-v-d-j","label":{"en":"Chromium Single Cell V(D)J"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"上記キットに準拠","en":"according to manufacturers' instructions"}},{"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":90,"unit":"bp","high":null,"suffix":{"ja":" (28×)","en":" (28×)"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch38","label":{"en":"GRCh38"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"以下の条件に該当するデータを除去\n- 発現遺伝子数： < 1000、もしくは > 4000\n- 総遺伝子発現カウント：< 2000、もしくは > 10,000\n- ミトコンドリアの割合：> 10%\n- TCR fragment genes","en":"the following criteria were excluded:\n- Number of expressed genes: < 1000 or > 4000\n- Total count of gene expression: < 2000 or > 10,000\n- Mitochondrial gene expression percentage: > 10%\n- TCR fragment genes"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"- Cell Ranger v6.1.2 (10x Genomics) with the \"multi\" option\n- Python package Scanpy v1.9.3（scRNA-seq解析）、Scirpy v0.13.0（TCR genotyping）","en":"- Cell Ranger v6.1.2 (10x Genomics) with the \"multi\" option\n- Python package Scanpy v1.9.3 (scRNA-seq analysis), Scirpy v0.13.0 (TCR genotyping)"}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":36601,"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":71457123136,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"csv","label":{"en":"CSV"}},{"code":"hdf5","label":{"en":"HDF5"}}]}