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GenomicsGenome-wide mapping of the transcription factor GABP-alpha binding in human CD34+CD133+ hematopoietic progenitor cells.
We used ChIP-Seq to map GABP-alpha binding sites in human hematopoietic progenitor cells (HPCs). Coupled with functional assays using GABP-alpha deficient mouse model and bioinformatics analysis, we systematically determined a transcriptional module controlled by GABP in HPCs. Examination of the rol...
ORGANISM(S): Homo sapiens 
2010-12-10 | E-GEOD-24933 | biostudies-arrayexpress
GenomicsGenome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors (ChIP-Seq)
Inactivating mutations in the MEN1 gene predisposing to the multiple endocrine neoplasia type 1 (MEN1) syndrome can also cause sporadic pancreatic endocrine tumors. MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase complexes that trimethylate histone H3 at lysine 4 (H3K...
ORGANISM(S): Mus musculus 
2012-06-01 | E-GEOD-37774 | biostudies-arrayexpress
GenomicsCTCF demarcates chromatin domains
Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates a...
ORGANISM(S): Homo sapiens 
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
GenomicsLdb1-nucleated transcription complexes function as primary mediators of erythroid gene activation
We used ChIP-Seq to map Ldb1, Scl and Gata1 binding sites in mouse total bone marrow cells. Together with functional studies comparing gene expression in Murine Erythroleukemia (MEL) cells expressing Ldb1 shRNA or control shRNA and bioinformatics analysis, we systematically determined the transcrip...
ORGANISM(S): Mus musculus 
2013-04-29 | E-GEOD-42843 | biostudies-arrayexpress
TranscriptomicsAcute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling]
The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESC...
ORGANISM(S): Mus musculus 
2012-01-06 | E-GEOD-34886 | biostudies-arrayexpress
TranscriptomicsAcute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
This SuperSeries is composed of the following subset Series: GSE34886: Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling] GSE34887: Acute depletion of Tet1-dependent 5-hydroxymethylcy...
ORGANISM(S): Mus musculus 
2012-01-04 | E-GEOD-34267 | biostudies-arrayexpress
TranscriptomicsesBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function
Signaling by the cytokine LIF and its downstream transcription factor, STAT3, prevents differentiation of pluripotent embryonic stem cells (ESCs) by opposing MAP kinase signaling. This contrasts with most cell types where STAT3 signaling induces differentiation. We find that STAT3 binding across t...
ORGANISM(S): Mus musculus 
2011-07-31 | E-GEOD-27708 | biostudies-arrayexpress
GenomicsHistone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [ChIP-seq]
Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-bindin...
ORGANISM(S): Mus musculus 
2014-08-14 | E-GEOD-56839 | biostudies-arrayexpress
GenomicsLIM domain binding protein 1 regulates a transcriptional program essential for hematopoietic stem cell maintenance
We used ChIP-Seq to map Ldb1, Scl and Gata2 binding sites in mouse hematopoietic progenitor cells (HPCs). Together with functional studies using conventional and conditional Ldb1 deficient mouse models and bioinformatics analysis, we systematically determined a transcriptional program controlled by ...
ORGANISM(S): Mus musculus 
2011-01-04 | E-GEOD-26031 | biostudies-arrayexpress
GenomicsAcute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [MRE-seq]
The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESC...
ORGANISM(S): Mus musculus 
2012-01-06 | E-GEOD-34887 | biostudies-arrayexpress
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