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GenomicsEffect of Ets1 knockdown in the P5424 thymic cell line
We performed ChIP-Seq for Ets1 and histone modifications in P5424 thymic cells, without and with Ets1 knockdown via shRNA. Overall, we find that loss of Ets1 results in specific, higher occupancy of H3K4me1-marked nucleosomes at the Ets1 binding site, but not H3K4me3 nucleosomes. We verified the spe...
ORGANISM(S): Mus musculus 
2015-12-19 | E-GEOD-74042 | biostudies-arrayexpress
GenomicsCpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters
This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manne...
ORGANISM(S): Mus musculus 
2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress
GenomicsThreonine-4 of Mammalian RNA Polymerase II CTD is Targeted by Polo-like Kinase-3 and Required for Transcriptional Elongation
Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5M-bM-^@M-^Y and 3M-bM-^@M-^Y regi...
ORGANISM(S): Homo sapiens 
2012-06-04 | E-GEOD-37519 | biostudies-arrayexpress
GenomicsTranscriptional landscape of Rag2 -/- thymocytes [Mnase-Seq]
We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene...
ORGANISM(S): Mus musculus 
2014-04-01 | E-GEOD-56360 | biostudies-arrayexpress
GenomicsTyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells
In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA matura...
ORGANISM(S): Homo sapiens 
2014-06-01 | E-GEOD-52914 | biostudies-arrayexpress
GenomicsTranscriptional landscape of Rag2 -/- thymocytes [ChIP-Seq]
We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene...
ORGANISM(S): Mus musculus 
2014-04-01 | E-GEOD-56393 | biostudies-arrayexpress
GenomicsSplicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 lysine 36
Several lines of recent evidence support a role for chromatin in splicing regulation. Here we show that splicing can also contribute to histone modification, which implies a bidirectional communication between epigenetics and RNA processing. Genome-wide analysis of histone methylation in human cell ...
ORGANISM(S): Homo sapiens 
2011-07-25 | E-GEOD-30902 | biostudies-arrayexpress
TranscriptomicsTranscription Initiation Platforms and GTF recruitment at tissue-specific enhancers and promoters
Recent works have shown that RNA Polymerase (Pol) II can be recruited to, and transcribe, distal regulatory regions. Here, we analyzed transcription initiation and elongation through genome-wide localization of Pol II, General Transcription Factors (GTFs) and active chromatin in developing T-cells. ...
ORGANISM(S): Mus musculus 
2011-05-20 | E-GEOD-29362 | biostudies-arrayexpress
TranscriptomicsGene expression analysis of Ets1-/- CD4+ CD8+ thymocytes
We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene...
ORGANISM(S): Mus musculus 
2015-12-19 | E-GEOD-73849 | biostudies-arrayexpress
GenomicsCpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (Phenantroline)
One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to gove...
ORGANISM(S): Homo sapiens 
2012-06-12 | E-GEOD-38564 | biostudies-arrayexpress
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