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GenomicsCapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals (ChIP-Seq)
Here we developed CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrated accurate quantification of enhan...
ORGANISM(S): Mus musculus 
2015-04-09 | E-GEOD-63732 | biostudies-arrayexpress
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
GenomicsH3K4 tri-methylation provides an epigenetic signature of active enhancers
Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K...
ORGANISM(S): Mus musculus 
2014-03-07 | E-GEOD-55635 | 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
TranscriptomicsThe TCR activation acts as a tumor suppressor mechanism in T-ALL
Developmental checkpoints in stem/progenitor cells are critical to the determination, commitment and differentiation into distinct lineages. Cancer cells often retain expression of lineage-specific checkpoint proteins, but their potential impact in cancer remains elusive. T lymphocytes mature in the...
ORGANISM(S): Homo sapiens 
2016-08-20 | E-GEOD-65496 | biostudies-arrayexpress
TranscriptomicsCapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals
Here we developed CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrated accurate quantification of enhan...
ORGANISM(S): Mus musculus 
2015-04-09 | E-GEOD-60029 | biostudies-arrayexpress
TranscriptomicsLong-range bidirectional transcription is a general feature of developmental gene promoters in mammals (RNA-Seq 1)
Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the R...
ORGANISM(S): Mus musculus 
2014-01-01 | E-GEOD-44232 | 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
GenomicsCpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq)
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-38563 | biostudies-arrayexpress
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