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TranscriptomicsThe tumor antigen PRAME is a substrate recognition subunit of a Cul2-based ubiquitin ligase and is associated with active NFY promoters
The human tumor antigen PRAME (Preferentially expressed antigen of melanoma) is frequently overexpressed in tumors. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in tumorigenesis remain largely elusive. We applied prote...
ORGANISM(S): Homo sapiens 
2011-07-29 | E-GEOD-26439 | biostudies-arrayexpress
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
GenomicsHigh resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq
This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip ...
ORGANISM(S): Mus musculus 
2009-06-06 | E-GEOD-15814 | 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 
TranscriptomicsSequencing of the non-ribosomal transcriptome allows the simultaneous identification of protein-coding and non-protein-coding RNAs
Deep Sequencing of protein-coding and non-protein-coding RNAs from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head Analysis of Ribominus RNA from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head There are no processed data files for GSM566806-GSM566811. ...
ORGANISM(S): Mus musculus 
2011-12-06 | E-GEOD-22959 | biostudies-arrayexpress
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
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
GenomicsChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3
This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates),...
ORGANISM(S): Homo sapiens 
2010-09-17 | E-GEOD-20303 | 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
TranscriptomicsRNA-Seq transcriptome profiling of in vitro cultures of migrating porcine primordial germ cells and porcine fetal fibroblasts of mini pig embryos between days 17-24 of gestation
Porcine embryonic germ cells (EGC) are cultured pluripotent cells derived from primordial germ cells (PGC). This study explored the possibilities to establish porcine EGC lines in the domestic breed pig more efficiently and from earlier embryonic stages than reported to date. In vitro culture of PGC...
ORGANISM(S): Sus scrofa 
2011-03-24 | E-GEOD-24220 | biostudies-arrayexpress
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