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

SyangArray

ABSTRACT: Gene expression was studied in the presence or absence of Otx2 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in undifferentiated and differentiated states.

ORGANISM(S): Mus musculus

SUBMITTER: Leo Leo Zeef

PROVIDER: E-MTAB-2239 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.

Yang Shen-Hsi SH Kalkan Tüzer T Morissroe Claire C Marks Hendrik H Stunnenberg Hendrik H Smith Austin A Sharrocks Andrew D AD

Cell reports 20140612 6

Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-renewing conditions but comparatively less about how cells exit from this state in response to differentiation stimuli. Here, we examined the role of Otx2 in this process in mouse ESCs and demonstrate that it plays a leading role in remodeling the gene re ...[more]

PMID: 24931607

Similar Datasets

syangRNAseq

Project description:Gene expression was studied in the presence or absence of Otx2 (RNAi) in the Rex1GFPd2 mouse embryonic stem cell line (parental line; E14Tg2a) in undifferentiated and differentiated states.

2014-06-24 | E-MTAB-2245 | biostudies-arrayexpress

Otx2 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Chromatin immunoprecipitation using Otx2 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2281 | biostudies-arrayexpress

Oct4 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Chromatin immunoprecipitation using Oct4 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2490 | biostudies-arrayexpress

FAIRE-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Formaldehyde-assisted isolation of regulatory elements (FAIRE) in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2283 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

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

2015-03-03 | E-GEOD-64059 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)

Project description:Gene regulatory elements such as enhancers have profound effects on cellular function, health, and disease. Our understanding of mammalian enhancer function is limited by the lack of a technology that would allow for a rapid and thorough test of their cell type-specific function. Here, we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells. Total RNA obtained from R26 dCas9-effector mESC lines after viral delivery of sgRNAs directed against proximal promoter or enhancer regions

2015-03-03 | E-GEOD-64057 | biostudies-arrayexpress

H3K27Ac and H3K4me1 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Chromatin immunoprecipitation using H3K27Ac and H3K4me1 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2282 | biostudies-arrayexpress

Expression data comparing transformed or neoplastic human neural precursors following OTX2 knockdown to transformed human neural precursor cells

Project description:Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies. We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following knockdown of OTX2 in transformed or neoplastic human embryonic neural precursor cells. OTX2 was knocked down in transformed human embyronic neural precursors (trans-hEN) using Silencer select siRNAs. trans-hEN OTX2 KD and scrambled control trans-hENs were then grown as neurospheres in defined medium and collected at passage 1. RNA was extracted using the Norgen All-in-One kit.

2015-08-25 | E-GEOD-66671 | biostudies-arrayexpress

Expression data comparing OTX2-overexpressing human neural precursors to human neural precursor cells

Project description:Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies. We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following overexpression of OTX2 in human embryonic neural precursor cells. OTX2 was stably overexpressed in human embyronic neural precursors (hEN) by lentiviral transduction. OTX2-hENs and control hENs were then grown as neurospheres in defined medium and collected at passage 2. RNA was extracted using the Norgen All-in-One kit.

2015-08-25 | E-GEOD-66670 | biostudies-arrayexpress

Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

Project description:The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE. Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.

2015-06-10 | E-GEOD-69724 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data