Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of EpiSCs undergoing reprogramming by Esrrb.

ABSTRACT: To characterize the reprogramming of epiblast stem cells (EpiSCs) into embryonic stem cells (ESCs) induced by Esrrb, we performed microarray analysis of Tet-on Esrrb EpiSCs after treatment with doxycycline (Dox).

ORGANISM(S): Mus musculus

SUBMITTER: Kenjiro Adachi

PROVIDER: E-MTAB-5341 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq analysis of Esrrb, Nanog, Oct4, and Sox2 in EpiSCs undergoing reprogramming

Project description:To investigate the molecular mechanisms underlying the reprogramming of epiblast stem cells (EpiSCs) into embryonic stem cells (ESCs) induced by Esrrb, we performed ChIP-seq analysis of Esrrb, Nanog, Oct4, and Sox2 in Tet-on Esrrb EpiSCs after treatment with doxycycline (Dox).

2018-06-01 | E-MTAB-5342 | biostudies-arrayexpress

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

BMP signaling in mouse embryonic stem cells (ESCs) in the naÃ¯ve and primed pluripotent states [RNA-Seq]

Project description:Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naÃ¯ve or primed states, we revisit the roles of BMP signaling in mESCs. RNA-seq analysis in 2 cell types; mESCs and ES-derived EpiSC (ESD-EpiSCs).

2015-12-04 | E-GEOD-70578 | biostudies-arrayexpress

Transcriptomic data of UCSF4 human embryonic stem cells (hESCs) and their neural derivatives

Project description:To compare transcriptomic profiles between UCSF4 hESCs and their neural derivatives, neural precursor cells (NPCs), we performed microarray analysis using the Affymetrix Human Gene 2.0 ST array platform. Six biological samples, three biological replicates for each developmental cell stage (in vitro)

2016-03-01 | E-GEOD-74378 | biostudies-arrayexpress

Zfp281 Coordinates Opposite Functions of Tet1 and Tet2 for Alternative Pluripotent States [RNA-Seq]

Project description:Pluripotent cell identity comprises a spectrum of cell states including naive and primed states, which are typified by mouse embryonic stem cells (ESCs) and epiblast-derived stem cells (EpiSCs), respectively. Here we define a pluripotent cell fate (PCF) gene signature based on RNA-seq analysis associated with naive and primed pluripotency acquisition, and identify Zfp281 as a key transcriptional regulator for primed pluripotency and also as a barrier to achieve the naive pluripotency of both mouse and human ESCs. RNA sequencing analysis was performed in WT and Zfp281 null mouse embryonic stem cells under different pluripotent culture conditions. RNA-seq Experiments were carry out in two biological replciates. Genome binding/occupancy profiling of Zfp281 was performed in mouse embryonic stem cells by ChIP sequencing.

2016-06-28 | E-GEOD-81044 | biostudies-arrayexpress

BMP signaling in mouse embryonic stem cells (ESCs) in the naÃ¯ve and primed pluripotent states

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-04 | E-GEOD-70581 | biostudies-arrayexpress

Global gene-expression analyses of the Esrrb knockdown cells

Project description:In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. These cells are also pluripotent and can differentiate in vitro and in vivo into the three major embryonic cell lineages. Furthermore, these cells contribute to mouse chimeras and are germline transmissible. In ES cells, Esrrb targets many genes involved in selfrenewal and pluripotency. This suggests that Esrrb may mediate reprogramming through the up-regulation of ES cell-specific genes. Our findings also indicate that it is possible to reprogram MEFs without exogenous Klf transcription factors and link a nuclear receptor to somatic cell reprogramming. Global gene expression effects of silencing the Esrrb gene. We used microarrays to detail the global programme of gene expression after silencing the Esrrb gene. Keywords: time-course Three biological replicates each for control GFP and Esrrb RNAi. The global gene expression profiles of the Esrrb knockdown cells were compared to control GFP knockdown cells for days 2, 4 and 6.

2010-06-24 | E-GEOD-13212 | 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. 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.

2013-10-17 | E-GEOD-28451 | biostudies-arrayexpress

ChIP-seq of MOF, MSL and NSL complex members in mouse ES cells and neuronal progenitors

Project description:We assessed the genome-wide binding of the histone acetylase MOF and members of its two associated complexes, the male-specific lethal and the non-specific lethal complex (MSL, NSL). We generated ChIP-seq profiles for MOF, MSL1, MSL2, KANSL3, and MCRS1 from mouse embryonic stem cells and neuronal progenitor cells. By using two replicates per sample and stringent filtering criteria, we identify five basic groups of genome regions where the proteins show either mutual or exclusive binding. We find that the NSL complex members (KANSL3, MCRS1) target the TSSs of broadly expressed genes with housekeeping functions in both cell types. MOF and particularly the MSL complex target a subset of these NSL-complex-targets, too. In addition, we find several thousand TSS-distal binding sites, particularly in ESCs, where KANSL3, MSL2 and MCRS1 show strong enrichments for annotated ESC enhancers. The vast majority of the binding to these ESC distal regulatory elements is lost in NPCs. Finally, we identify mostly intronic and intergenic regions with predominant MSL2 enrichments without the presence of its known interactors. These binding sites do not overlap with ESC marks of active chromatin (e.g. DNase hypersensitivity sites), but the they increase in number upon differentiation and we detect a strong signature of the (CAGA)n motif. Our study provides the first comprehensive analysis of MOF in the context of its two complexes in the mouse and reveals shared as well as distinct and dynamic functions for gene regulation and pluripotency. ChIP-seq of MOF and members of its associated complexes (MSL complex: MSL1, MSL2; NSL complex: KANSL3, MCRS1) in male mouse embryonic stem cells and neuronal progenitor cells derived from them.

2014-06-03 | E-GEOD-51746 | biostudies-arrayexpress

Zfp281 Coordinates Opposite Functions of Tet1 and Tet2 for Alternative Pluripotent States

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-28 | E-GEOD-81045 | biostudies-arrayexpress