{"id":"hum0115","version":1,"url":"https://humandbs.dbcls.jp/research/hum0115/v1","datePublished":"2020-05-15","versions":[{"version":1,"datePublished":"2020-05-15"}],"title":{"ja":"動的遺伝子ネットワークの多次元構造解析による高精度な細胞分化制御技術の開発","en":"Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks"},"summary":{"aims":{"ja":"転写因子などの外来性遺伝子カセットを誘導したトランスクリプトームの解析","en":"Transcriptome analyses for transgene induced ES cell (TF-hESC) lines which carry open reading frame (ORF) of transcriptional factors (TFs)."},"methods":{"ja":"RNAシーケンスおよびマイクロアレイ解析","en":"RNA sequencing and Microarray assay"},"targets":{"ja":"SEES3に外来性遺伝子（主にtranscriptional factor：TF）を導入して樹立したES細胞株（TF-hESC）。\n＜RNA-seq＞\n437種類のTFを導入した独立株2種（品質解析の結果、遺伝子誘導が十分でない株については1株）を樹立し、TF誘導後もしくは非誘導条件で48時間後（1774株）、および、指定された時間培養した複数点（406株）、計2300検体分のデータ（437遺伝子×2株（一部1株）×2条件以上）。\n＜マイクロアレイ解析＞\n116種類のTFを導入した独立株2種（品質解析の結果、遺伝子誘導が十分でない株については1株）を樹立し、TF誘導後もしくは非誘導条件で48時間培養した、計448検体分のデータ（116遺伝子×2株（一部1株）×2条件）。","en":"Transcriptome data of each transcriptional factor induced human embryonic stem cell (TF-hESC) lines which were derived from SEES3.\n<RNA-seq data>\nEach TF-hESC line was specifically induced in response to 437 transgenes (almost all of them were categorized as transcriptional factor: TF). Each line has biological replicate from two independent clones (some are missing replicates because of poor gene inductions). Each data was obtained from cell culture with or without TF induction, at 48-hour , or multiple time points. As total, 2300 samples were analyzed in parallel experiments (437 genes x [1 or 2 clones] x [2 or more culture conditions]).\n<microarray data>\nEach TF-hESC line was specifically induced in response to 116 transgenes (almost all of them were categorized as transcriptional factor: TF). As total, 448 samples were obtained from 48-hour culture with or without transgene induction (116 genes x [1 or 2 clones] x 2 culture conditions)."},"url":{"ja":[{"url":"https://www.jst.go.jp/kisoken/crest/en/project/35/e35_04.html","text":"https://www.jst.go.jp/kisoken/crest/en/project/35/e35_04.html"}],"en":null}},"listingSummary":{"methods":{"ja":"発現","en":"Expression profiling"},"targets":{"ja":"SEES3にTFを導入して樹立したES細胞株（TF-hESC）\n（細胞株）","en":"TF-hESCs derived from SEES3\n(Cell-line)"},"typeOfData":{"ja":"NGS\n（RNA-seq）\nマイクロアレイ","en":"NGS\n(RNA-seq)\nMicroarray"}},"releaseNote":{"ja":"SEES 3に外来性遺伝子（主にtranscriptional factor：TF）を導入して樹立したES細胞株（TF-hESC）の発現データを提供する。RNA-seqでは計2300検体分のデータ（437遺伝子×2株（一部1株）×2条件以上）を非制限公開データとしてfastqファイルを、マイクロアレイ解析では計448検体分のデータ（116遺伝子×2株（一部1株）×2条件）を制限公開データとしてtxtファイルを、それぞれ提供する。\nTFを導入したSEES3細胞から樹立したTF-hESCについて、それぞれの誘導および培養条件で培養した細胞からmRNAを抽出。SureSelect Strand Specific RNA Library Preparation Kit for Illumina（Agilent Technologies）を用いてRNA-seqのライブラリーを作成後、Illumina [HiSeq 2000/2500]により平均長50 bp（Single-end）、202もしくは302 bp（Paired-end）を読んだ。また、上記mRNAを対象とした、Agilent SurePrint G3 Human GE v2 8x60K Microarrayによるマイクロアレイ解析結果（補正前のintensityデータ）を提供する。","en":"Transcriptome data of transcriptional factor (TF) induced human embryonic stem cell (TF-hESC) lines which were derived from SEES3 are provided. RNA-seq data from total of 2300 samples (437 genes x [1 or 2 lines] x [2 or more culture conditions]) are provided as unrestricted access data (fastq), and microarray intensity data from total of 448 samples (116 genes x [1 or 2 lines] x 2 culture condition) are provided as controlled-access data (txt).\nmRNAs were extracted from each TF-hESC line under a few culture conditions. Libraries for RNA-seq were prepared using SureSelect Strand Specific RNA Library Preparation Kit for Illumina (Agilent Technologies) and RNA-seq was performed with Illumina [HiSeq 2000/2500] (single-end : 50 bp, paired-end : 202 or 302 bp). Microarray analysis was performed by using of Agilent SurePrint G3 Human GE v2 8x60K Microarray."},"dataProviders":[{"name":{"ja":"洪 実","en":"Minoru S.H. Ko"},"organization":{"name":{"ja":"慶應義塾大学医学部 坂口光洋記念システム医学講座","en":"Department of Systems Medicine, Mitsunada SakaguchiLaboratory, Keio University School of Medicine"}}}],"researchProjects":[{"name":{"ja":"JST CREST：研究領域「生命動態の理解と制御のための基盤技術の創出」 / 洪グループ「動的遺伝子ネットワークの多次元構造解析による高精度な細胞分化制御技術の開発」","en":"JST CREST: Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics / Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks"},"url":{"ja":[{"url":"https://www.jst.go.jp/kisoken/crest/project/35/35_04.html","text":"https://www.jst.go.jp/kisoken/crest/project/35/35_04.html"}],"en":[{"url":"https://www.jst.go.jp/kisoken/crest/en/project/35/e35_04.html","text":"https://www.jst.go.jp/kisoken/crest/en/project/35/e35_04.html"}]}}],"grants":[{"title":{"ja":"動的遺伝子ネットワークの多次元構造解析による高精度な細胞分化制御技術の開発","en":"Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks"},"agency":{"ja":"CREST/生命動態の理解と制御のための基盤技術の創出","en":"CREST / Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics"},"grantIds":["JPMJCR12W4"]}],"relatedPublications":[{"title":"Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors","doi":"https://doi.org/10.1016/j.celrep.2020.107655","datasets":["JGAD000132","DRA006296"]}],"datasets":["JGAD000132","DRA006296"],"controlledAccessUsers":[]}