Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines

Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro , and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mou...

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Veröffentlicht in:	Scientific reports Jg. 6; H. 1; S. 25667
Hauptverfasser:	Yamamizu, Kohei, Sharov, Alexei A., Piao, Yulan, Amano, Misa, Yu, Hong, Nishiyama, Akira, Dudekula, Dawood B., Schlessinger, David, Ko, Minoru S. H.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London Nature Publishing Group UK 06.05.2016 Nature Publishing Group
Schlagworte:	13 13/100 38/39 42 631/532/2117 631/553 631/80 64/60 Animals Biomarkers - metabolism Cell differentiation Cell Differentiation - genetics Cell Line Cell lines Doxycycline Embryo cells Gene expression Gene Expression Profiling Gene Expression Regulation Gene Ontology Humanities and Social Sciences Islet-1 protein Leukocytes Mice Mouse Embryonic Stem Cells - metabolism multidisciplinary Organ Specificity - genetics Phenotype Protein Binding - genetics Reproducibility of Results Science Science (multidisciplinary) Stem cell transplantation Stem cells Transcription factors Transcription Factors - metabolism Transcriptome - genetics
ISSN:	2045-2322, 2045-2322
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Abstract	Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro , and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this “NIA Mouse ESC Bank,” we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1 , and St18 ; mesodermal lineages by Pitx1 , Pitx2 , Barhl2 , and Lmx1 a; white blood cells by Myb , Etv2 , and Tbx6 , and ovary by Pitx1 , Pitx2 , and Dmrtc2 ). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.
AbstractList	Mouse embryonic stem cells (ESCs) can differentiate into a wide range - and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this "NIA Mouse ESC Bank," we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs. Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro , and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this “NIA Mouse ESC Bank,” we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1 , and St18 ; mesodermal lineages by Pitx1 , Pitx2 , Barhl2 , and Lmx1 a; white blood cells by Myb , Etv2 , and Tbx6 , and ovary by Pitx1 , Pitx2 , and Dmrtc2 ). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs. Mouse embryonic stem cells (ESCs) can differentiate into a wide range - and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this "NIA Mouse ESC Bank," we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.Mouse embryonic stem cells (ESCs) can differentiate into a wide range - and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this "NIA Mouse ESC Bank," we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.
ArticleNumber	25667
Author	Piao, Yulan Amano, Misa Yamamizu, Kohei Ko, Minoru S. H. Dudekula, Dawood B. Nishiyama, Akira Yu, Hong Schlessinger, David Sharov, Alexei A.
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Cites_doi	10.1093/nar/gkr1048 10.1242/dev.00192 10.1038/ni.1865 10.1146/annurev-cellbio-100913-013116 10.1016/j.stemcr.2013.10.006 10.1016/j.diff.2012.04.007 10.1016/j.stem.2009.07.012 10.1186/1471-2105-6-144 10.1089/cmb.2013.0126 10.1371/journal.pgen.1004280 10.1186/gb-2005-6-7-r61 10.1186/1755-8794-3-1 10.1161/ATVBAHA.114.304768 10.1038/srep00167 10.1161/CIRCGENETICS.113.000259 10.1002/dvdy.24091 10.1038/srep01390 10.1016/j.bbrc.2004.07.179 S0006-291X(04)01714-0 10.1186/gb-2009-10-11-r130 10.1073/pnas.012025199012025199 10.1016/j.ydbio.2014.09.027 10.1073/pnas.1112392109 10.1074/jbc.M114.566448 10.1371/journal.pone.0000026 10.1038/nn.3467 10.15252/embr.201439939 10.1016/j.cell.2013.07.034 10.1093/nar/gni043 10.1093/bioinformatics/bti343 10.1371/journal.pgen.1005375 10.1016/j.ydbio.2012.11.017 10.1142/S0219720015500195
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Snippet	Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro , and thus provide an ideal platform to study... Mouse embryonic stem cells (ESCs) can differentiate into a wide range - and possibly all cell types in vitro, and thus provide an ideal platform to study... Mouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro, and thus provide an ideal platform to study...
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SubjectTerms	13 13/100 38/39 42 631/532/2117 631/553 631/80 64/60 Animals Biomarkers - metabolism Cell differentiation Cell Differentiation - genetics Cell Line Cell lines Doxycycline Embryo cells Gene expression Gene Expression Profiling Gene Expression Regulation Gene Ontology Humanities and Social Sciences Islet-1 protein Leukocytes Mice Mouse Embryonic Stem Cells - metabolism multidisciplinary Organ Specificity - genetics Phenotype Protein Binding - genetics Reproducibility of Results Science Science (multidisciplinary) Stem cell transplantation Stem cells Transcription factors Transcription Factors - metabolism Transcriptome - genetics
Title	Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines
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