{"id":"JGAD000960","research":"hum0512","url":"https://humandbs.dbcls.jp/dataset/JGAD000960","datePublished":"2025-07-31","dateModified":"2025-10-27","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":"健常者 3 名の CD4+ / CD3+ T 細胞に対する LEF1 ノックダウン後の bulk RNA-seq / bulk ATAC-seq / scCITE-seq データ。","en":"bulk RNA-seq / bulk ATAC-seq / scCITE-seq of CD4+ / CD3+ T cells from 3 healthy donors following LEF1 siRNA knockdown."}}],"experiments":[{"label":"bulk RNA-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"健常者：3名\n単離したCD4+ T細胞をCD3/CD28で活性化した上でIL-2培地にて培養後、LEF1 siRNAもしくはコントロールsiRNAによりノックダウン後、24時間後、48時間後、72時間後の1サンプルずつ 合計18サンプル","en":"3 healthy donors\nCD4+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 24, 48, and 72 hours post-knockdown.\n1 sample each, total 18 samples"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"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":"age-group","label":{"ja":"年齢層","en":"Age group"},"type":"vocabulary","terms":[{"code":"adult","label":{"ja":"成人","en":"Adult"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"CD4+ T細胞より抽出したRNA","en":"RNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"cd4-t-cell","label":{"ja":"CD4 陽性 T 細胞","en":"CD4+ T cell"}}]},{"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":"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":"smart-seq-mrna","label":{"en":"SMART-Seq mRNA"}},{"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","en":"Nextera XT"}},{"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":100,"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":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"FastQC for raw reads; Nextera adapter trimming (min 20bp);\nRNASeQC2 for alignment metrics","en":"FastQC for raw reads; Nextera adapter trimming (min 20bp);\nRNASeQC2 for alignment metrics"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"STAR（v2.7.9a）\nRNA-SeQC2（v2.4.2）","en":"STAR(v2.7.9a)\nRNA-SeQC2(v2.4.2)"}},{"key":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"not-included","label":{"ja":"なし","en":"Not included"}}]},{"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":"bulk ATAC-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"健常者：3名\n単離したCD4+ T細胞をCD3/CD28で活性化した上でIL-2培地にて培養後、LEF1 siRNAもしくはコントロールsiRNAによりノックダウン後、24時間後、48時間後、72時間後の1サンプルずつ 合計18サンプル","en":"3 healthy donors\nCD4+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 24, 48, and 72 hours post-knockdown.\n1 sample each, total 18 samples"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"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":"age-group","label":{"ja":"年齢層","en":"Age group"},"type":"vocabulary","terms":[{"code":"adult","label":{"ja":"成人","en":"Adult"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"CD4+ T細胞より抽出したDNA","en":"DNAs extracted from CD4+ T cells transfected with LEF1-specific siRNA or control siRNA"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"cd4-t-cell","label":{"ja":"CD4 陽性 T 細胞","en":"CD4+ T cell"}}]},{"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":"atac-seq","label":{"en":"ATAC-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":"nextera-xt-index-kit-v2","label":{"en":"Nextera XT Index Kit v2"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"Tn5 tagmentation with Nextera kit","en":"Tn5 tagmentation with Nextera kit"}},{"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":100,"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":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"FastQC for raw reads; Nextera adapter trimming (min 20bp);\nBAM filtering (samtools -F 1804 -f 2 -q 30);\nBlacklist removal;\nMACS2 peak calling (q<0.05);\nATACseqQC TSS enrichment score; ataqv metrics;","en":"FastQC for raw reads; Nextera adapter trimming (min 20bp);\nBAM filtering (samtools -F 1804 -f 2 -q 30);\nBlacklist removal;\nMACS2 peak calling (q<0.05);\nATACseqQC TSS enrichment score; ataqv metrics;"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Bowtie2（v2.2.6）\nMACS2（v2.2.7.1）","en":"Bowtie2 (v2.2.6)\nMACS2 (v2.2.7.1)"}},{"key":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"not-included","label":{"ja":"なし","en":"Not included"}}]},{"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":"scCITE-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"健常者：3名\n単離したCD3+ T細胞をCD3/CD28で活性化した上でIL-2培地にて培養後、LEF1 siRNAもしくはコントロールsiRNAによりノックダウン後、48時間後、72時間後の1サンプルずつ 合計12サンプル（3名をプールして実施）","en":"3 healthy donors\nCD3+ T cells isolated from donors were activated with CD3/CD28 Dynabeads and cultured in media containing IL-2. Cells were transfected with LEF1-specific siRNA or control siRNA, and harvested at 48 and 72 hours post-knockdown.\n1 sample each, total 12 samples (Samples from 3 donors were pooled.)"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"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":"age-group","label":{"ja":"年齢層","en":"Age group"},"type":"vocabulary","terms":[{"code":"adult","label":{"ja":"成人","en":"Adult"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"CD3+ T細胞より抽出した細胞表面タンパク質とpolyA RNA","en":"RNAs extracted from CD3+ T cells isolated from samples"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"cd3-t-cell","label":{"en":"CD3+ T cell"}}]},{"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":"cite-seq","label":{"en":"CITE-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-5-v2","label":{"en":"Chromium Next GEM Single Cell 5' v2"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"Standard protocol of 10x Genomics","en":"Standard protocol of 10x Genomics"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-novaseq-x-plus","label":{"en":"Illumina NovaSeq X Plus"}},{"code":"10x-genomics-chromium","label":{"en":"10x Genomics Chromium"}}]},{"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":151,"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":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"detected genes, UMI counts, mitochondrial gene percentage,\ndoublet detection","en":"detected genes, UMI counts, mitochondrial gene percentage,\ndoublet detection"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Cell Ranger 7.0.1","en":"Cell Ranger 7.0.1"}},{"key":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"not-included","label":{"ja":"なし","en":"Not included"}}]},{"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":631571822539,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"tsv","label":{"en":"TSV"}},{"code":"mtx","label":{"en":"MTX"}},{"code":"hdf5","label":{"en":"HDF5"}}]}