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GenomicsLigand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating Retinoic Acid Receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the ret...
ORGANISM(S): Mus musculus 
2010-12-10 | E-GEOD-19409 | biostudies-arrayexpress
GenomicsInduced Cdx2 binding in embryonic stem cells and endodermal cells
Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGP...
ORGANISM(S): Mus musculus 
2014-03-27 | E-GEOD-39435 | biostudies-arrayexpress
GenomicsRapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2012-12-13 | E-GEOD-19450 | biostudies-arrayexpress
TranscriptomicsInduced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2013-07-04 | E-GEOD-39453 | biostudies-arrayexpress
GenomicsA Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis
Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling...
ORGANISM(S): Danio rerio 
2013-12-02 | E-GEOD-48254 | biostudies-arrayexpress
GenomicsEmbryonic stem cell based system for the discovery and mapping of developmental transcriptional programs
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the method of choice to study function of transcription factors in cell fate determination. This technique faces two major obstacles when applied to developmental studies: the availability of ChIP grade antibodies and access to ...
ORGANISM(S): Mus musculus 
2011-11-12 | E-GEOD-30882 | biostudies-arrayexpress
GenomicsHoxc9 ChIP-seq in differentiating motor neurons
The expression of v5-tagged Hoxc9 is induced and ChIP-seq is used to profile genome-wide occupancy in differentiating motor neurons The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid and hedgehog signaling. Here, ChIP-seq is used to pr...
ORGANISM(S): Mus musculus 
2010-09-08 | E-GEOD-21812 | biostudies-arrayexpress
GenomicsInduced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains [ChIP-Seq]
We aim to understand the role that Cdx2 plays in specifying the rostro-caudal identity of differentiating motor neurons. We find that expressing Cdx2 in combination with FGF signaling is sufficient to produce motor neurons with a more caudal identity. ChIP-seq analysis of Cdx2 finds that it binds ex...
ORGANISM(S): Mus musculus 
2013-07-04 | E-GEOD-39433 | biostudies-arrayexpress
TranscriptomicsInduced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains [Affymetrix]
We aim to understand the role that Cdx2 plays in specifying the rostro-caudal identity of differentiating motor neurons. We find that expressing Cdx2 in combination with FGF signaling is sufficient to produce motor neurons with a more caudal identity. ChIP-seq analysis of Cdx2 finds that it binds ex...
ORGANISM(S): Mus musculus 
2013-07-04 | E-GEOD-39422 | biostudies-arrayexpress
GenomicsChromatin landscape of progenitor motor neurons [ChIP-seq]
Progenitor motor neurons can be generated with high-efficiency by differentiating ES cells in vitro in the presence of retinoic acid and hedgehog signalling. Here, we characterize the chromatin landscape associated with progenitor motor neurons (pMNs) in order to assess how histone modification doma...
ORGANISM(S): Mus musculus 
2013-07-04 | E-GEOD-39434 | biostudies-arrayexpress
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