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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Conditional knockout of Sox2 in embryonic and trophoblast stem cells.

ABSTRACT: To compare the transcriptional networks governed by Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Sox2 in each cell type. A Tet-inducible Sox2 knockout ES cell line 2TS22C or its derivative TSC line 22CEROH2-TSC1 were treated with Tet for 4 days. A total of 12 samples from ES or TS cells cultured with or without Tet were analyzed in three biological replicates.

ORGANISM(S): Mus musculus

SUBMITTER: Itoshi NIKAIDO

PROVIDER: E-GEOD-28451 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.

Adachi Kenjiro K Nikaido Itoshi I Ohta Hiroshi H Ohtsuka Satoshi S Ura Hiroki H Kadota Mitsutaka M Wakayama Teruhiko T Ueda Hiroki R HR Niwa Hitoshi H

Molecular cell 20131010 3

Sox2 is a transcription factor required for the maintenance of pluripotency. It also plays an essential role in different types of multipotent stem cells, raising the possibility that Sox2 governs the common stemness phenotype. Here we show that Sox2 is a critical downstream target of fibroblast growth factor (FGF) signaling, which mediates self-renewal of trophoblast stem cells (TSCs). Sustained expression of Sox2 together with Esrrb or Tfap2c can replace FGF dependency. By comparing genome-wid ...[more]

PMID: 24120664

Similar Datasets

Sox2-regulatory networks in embryonic and trophoblast stem cells.

Project description:Sox2 is a pleiotropic transcription factor that regulates self-renewal and differentiation capacity in different types of stem cells, raising the possibility that it regulates similar transcriptional programs controlling common stemness. Embryonic stem (ES) cells and trophoblast stem (TS) cells are two developmentally related types of stem cells, which originate from distinct lineages of peri-implantation embryos. We have found that Sox2 is a critical regulator of self-renewal in both of two stem cells. Genome-wide analysis of Sox2 target genes using Affymetrix Exon Arrays and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) unraveled that it regulates distinct transcriptional networks in ES and TS cells. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-17 | E-GEOD-28455 | biostudies-arrayexpress

Induction of trophoblast stem cells from embryonic stem cells by forced repression of Oct3/4.

Project description:To characterize the transdifferentiation of embryonic stem (ES) cells into trophoblast stem (TS) cells triggered by forced repression of Oct3/4, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Oct3/4. A Tet-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs). A total of 15 samples from Day 0 to Day 4 were analyzed in three biological replicates.

2013-10-17 | E-GEOD-28452 | biostudies-arrayexpress

Dynamics of Sox2 occupancy during the differentiation of embryonic stem cells into trophoblast stem cells.

Project description:To understand the mechanism underlying the versatility in transcriptional regulation by Sox2, we compared genome-wide binding sites of Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). A tetracycline-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs).

2013-10-17 | E-GEOD-28453 | biostudies-arrayexpress

ChIP-seq anlysis of Sox2, Tfap2c, and Cdx2 in trophoblast stem cells.

Project description:To understand the mechanism underlying the transcriptional regulation by Sox2, we analyzed genome-wide binding sites of Sox2, Tfap2c, and Cdx2 in trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). ZHBTc4- and embryo-derived TS cell lines were maintained in the presence of FGF4 and mouse embryonic fibroblasts (MEFs).

2014-01-03 | E-GEOD-51511 | biostudies-arrayexpress

Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast [MeDIP-Seq]

Project description:Reprogramming of ES cells towards the trophoblast lineage, and specifally into self-renewing TS cells, can seemingly be achieved by manipulation of transcription factors such as Cdx2 and Oct4, or modulation of signalling cascades, notably Ras signalling. Here we analyze the arising cells from such treatment in detail for the efficiency and completeness of the reprogramming process. We find that the reprogrammed cells retain an epigenetic and transcriptional memory of their ES cell origin and are not equal to bona fide trophectoderm-derived TS cells. DNA methylation analysis in conventional ES and TS cells and various ES-to-TS reprogramming models

2014-11-24 | E-GEOD-62138 | biostudies-arrayexpress

Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast [RNA-Seq]

Project description:Reprogramming of ES cells towards the trophoblast lineage, and specifally into self-renewing TS cells, can seemingly be achieved by manipulation of transcription factors such as Cdx2 and Oct4, or modulation of signalling cascades, notably Ras signalling. Here we analyze the arising cells from such treatment in detail for the efficiency and completeness of the reprogramming process. We find that the reprogrammed cells retain an epigenetic and transcriptional memory of their ES cell origin and are not equal to bona fide trophectoderm-derived TS cells. RNA-seq expression analysis in conventional ES and TS cells and various ES-to-TS reprogramming models

2014-11-24 | E-GEOD-62149 | biostudies-arrayexpress

Conditional knockout of Sox2 in embryonic and trophoblast stem cells.

Project description:To compare the transcriptional networks governed by Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Sox2 in each cell type.

2013-10-17 | GSE28451 | GEO

Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression

Project description:POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks. Keywords: development or differentiation design,time series design ZHBTc4, ZHTc6, and EB5 ES cells were cultured without feeder cells in LIF-supplemented medium as described . For differentiation, ZHTc6 cells were cultured in the absence of Tet, which induced the overexpression of Oct3/4. ZHBTc4 cells were cultured in the presence of Tet, repressing Oct3/4 expression. Trophoblast stem (TS) cells and another ES cell line (R1) were cultured as previously described . Three independent samples were prepared for each time point. Microarray experiments were carried out as described using the NIA Mouse 22K Microarray v1.0.

2010-06-30 | E-GEOD-5936 | biostudies-arrayexpress

Expression data from day 3 Flk-1 mesoderm between ER71 overexpressed and ER71 knockout mouse embryonic stem cell

Project description:Ets transcription factor ER71 is critical for Flk-1 mesoderm specification to different cell lineages. In this dataset, we determine to investigate the mechanisms by which ER71 regulates hematopoietic and endothelial cell versus cardiac cell lineage development. Expression of all four Flk-1+ mesoderm populations (i.e. Er71 overexpressed versus control, Er71 deficient versus control Flk-1+ mesoderm) was compared. Specifically, we sorted Flk-1+ mesoderm from day 3 differentiated embryonic stem(ES) cells, including induced Er71 and control ES cells, as well as Er71+/+ as well as Er71-/- ES cells .

2012-02-20 | E-GEOD-35793 | biostudies-arrayexpress

Expression data throughout reprogramming of MEF to iPS using a Dox-inducible promoter

Project description:6C secondary MEFs were treated with Dox in mES media to turn on the Oct4, Klf4, cMyc, Sox2. Total RNA was extracted at day 0 (no Dox), day2, 5, 8, 11, 16 and 21 (with Dox) and day 30 (Dox-independent secondary iPS). RNA from Parental MEFs and Primary-iPS cells were also extracted for reference. 1B secondary MEFs were Dox treated for 5-days followed by RNA extraction. Subsequently, a culture removed of Dox treatment for an additional 5days was also analyzed. Samples from 6C-clones were smoothed using a polynomial fitting. Subsequently, phase analysis was carried out based on point of change greater than 2-fold.

2010-07-30 | E-GEOD-21757 | biostudies-arrayexpress

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