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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
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
TranscriptomicsTranscriptome study of P5424 T-cell line
P5424 T-cell line was observed transcriptome in two replicates Total RNAs were extracted from 2 samples of P5424 T-cell line and were profiled in replicate after hybridization with Agilent SurePrint G3 Mouse GE 8x60K
ORGANISM(S): Mus musculus 
2015-04-09 | E-GEOD-63731 | 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
TranscriptomicsTranscriptional landscape of Rag2 -/- thymocytes [ShortRNA-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-56358 | biostudies-arrayexpress
TranscriptomicsGene expression analysis of CD4+ CD8+ thymocytes [Affymetrix]
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-56357 | 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
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
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