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TranscriptomicsDynamic binding of RBPJ is determined by Notch signalling status
Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription ...
ORGANISM(S): Mus musculus 
2013-05-13 | E-GEOD-37184 | biostudies-arrayexpress
ProteomicsA quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood
The interaction between transcription factors and genomic DNA forms the basis for spatio-temporal control of gene expression. Therefore, these interactions and their impact on disease and cellular fate are extensively studied on a global level, mainly using techniques based on next-generation sequen...
ORGANISM(S): Homo sapiens (Human) 
2015-01-05 | PXD000782 | Pride
Blood Pbmcs Dna pull-down Primary cells 
Genomics5-hydroxymethylcytosine: the sixth DNA base
We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) pr...
ORGANISM(S): Mus musculus 
2011-11-24 | E-GEOD-31343 | biostudies-arrayexpress
GenomicsGenome wide profiling of MBD2 binding
We show that in vivo MBD2 is mainly recruited to CpG island promoters that are highly methylated. We also report that MBD2 binds to a subset of CpG island promoters that are characterized by the presence of active histone marks and RNA polymerase II (Pol2). At such sites, MBD2 binds downstream of th...
ORGANISM(S): Homo sapiens 
2014-07-03 | E-GEOD-54693 | biostudies-arrayexpress
GenomicsOncofusion protein AML1-ETO targets ERG factor binding sites in AML
ERG has been identified as an essential factor for the function and maintenance of adult hematopoietic stem cells and high ERG expression is a negative prognostic marker for treatment outcome in AML. The molecular function of ERG and its interplay with other factors is however largely unknown. Here ...
ORGANISM(S): Homo sapiens 
2012-09-18 | E-GEOD-23730 | biostudies-arrayexpress
GenomicsSequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively ...
ORGANISM(S): Homo sapiens 
2012-03-27 | E-GEOD-28254 | biostudies-arrayexpress
TranscriptomicsA compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes
Different mechanisms for CBF-MYH11 function in acute myeloid Leukemia (AML) with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of ...
ORGANISM(S): Homo sapiens 
2013-09-09 | E-GEOD-46044 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of mouse embryonic stem cells treated with MS-275
This study describes transcriptome profiling of mouse ES cells treated with MS-275. We included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA RNA-Seq profiling on mouse ES cells treated with MS-275
ORGANISM(S): Mus musculus 
2014-03-28 | E-GEOD-45909 | biostudies-arrayexpress
ProteomicsPlasmodium falciparum bromo-domain containing epigenetic protein complexes recruited to modified histone tails as identified by histone peptide pulldown (HPP)-MS/MS and further characterized by GFP-IP-MS/MS and HA-IP-MS/MS
In order to identify epigenetic protein complexes recruited to histone PTMs in the deadly human malaria parasite Plasmodium falciparum, we set out to perform histone peptide pulldowns with various histone peptides. Biotinylated peptides corresponding to P. falciparum histone variant H2A.Z, H2B.Z and...
ORGANISM(S): Plasmodium falciparum 
2019-10-15 | PXD010644 | Pride
Epigenetic complex Bromo-domain protein Hpp Gcn5 Gfp-ip Histone peptide pulldown Interactor Plasmodium falciparum Taf1 Histone acetylation Ha-ip Reader complex Histone methylation 
TranscriptomicsMll2 is required for H3K4 trimethylation on bivalent promoters in ES cells whereas Mll1 is redundant
Trimethylation of histone 3 lysine 4 (H3K4me3) at promoters of actively transcribed genes is a universal epigenetic mark and a key product of Trithorax-Group action. Here we show that Mll2, one of the six Set1/Trithorax-type H3K4 methyltransferases in mammals, is required for trimethylation of bival...
ORGANISM(S): Mus musculus 
2014-01-20 | E-GEOD-52071 | biostudies-arrayexpress
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