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TranscriptomicsIdentification of ploidy-regulated genes in budding yeast
Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy. Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (M...
ORGANISM(S): Saccharomyces cerevisiae 
2010-11-04 | E-GEOD-19685 | 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
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
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
GenomicsDNase I hypersensitivity and algorithmic prediction of TF binding in early pancreatic mES directed differentiation
This dataset uses DNase-seq to profile the genome-wide DNase I hypersensitivity of mES and mES-derived cells along an early pancreatic lineage and provides the locations of putative Transcription Factor (TF) binding sites using the PIQ algorithm. DNase-seq takes advantage of the preferential cutting...
ORGANISM(S): Mus musculus 
2014-01-19 | E-GEOD-53776 | biostudies-arrayexpress
TranscriptomicsTranscription profiling, Rpd3 ChIP-chip and histone H4 and TATA binding protein ChIP-chip of wild type, cti6 and sfl1 yeast mutants
Effects of genetic modification of trans-acting transcription factors and a chromatin remodeler on noncoding RNA transcription and trans-acting factor binding at loci in yeast.
ORGANISM(S): Saccharomyces cerevisiae 
2010-03-29 | E-MEXP-2269 | 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
TranscriptomicsTranscription profiling of Arabidopsis FACS sorted root specific cell types after nitrogen treatment
The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a g...
ORGANISM(S): Arabidopsis thaliana 
2008-06-15 | E-GEOD-7631 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human HNF3b and E2F4, and mouse NeuroD1, for THEME analysis
Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the disco...
ORGANISM(S): Mus musculus 
2006-05-09 | E-WMIT-8 | biostudies-arrayexpress
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