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GenomicsCo-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in ma...
ORGANISM(S): Mus musculus 
2014-05-08 | E-GEOD-50762 | biostudies-arrayexpress
TranscriptomicsA large fraction of extragenic RNA Pol II transcription sites overlap enhancers
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are product...
ORGANISM(S): Mus musculus 
2010-05-21 | E-GEOD-20370 | biostudies-arrayexpress
GenomicsA large fraction of extragenic RNA Pol II transcription sites overlap enhancers (2)
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are product...
ORGANISM(S): Mus musculus 
2010-05-21 | E-GEOD-19991 | biostudies-arrayexpress
GenomicsIdentification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages
Enhancers determine tissue-specific gene expression programs. Enhancers are marked by high histone H3 lysine 4 mono-methylation (H3K4me1) and by the acetyl-transferase p300, which has allowed genome-wide enhancer identification. However, the regulatory principles by which subsets of enhancers become...
ORGANISM(S): Mus musculus 
2010-03-05 | E-GEOD-19553 | biostudies-arrayexpress
TranscriptomicsMechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes (Illumina sequencing data)
Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies tha...
ORGANISM(S): Mus musculus 
2011-01-01 | E-GEOD-23619 | biostudies-arrayexpress
GenomicsLatent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (ChIP-seq)
According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in t...
ORGANISM(S): Mus musculus 
2013-01-17 | E-GEOD-38377 | biostudies-arrayexpress
TranscriptomicsLatent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (RNA-seq)
According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in t...
ORGANISM(S): Mus musculus 
2013-01-17 | E-GEOD-38371 | biostudies-arrayexpress
GenomicsLatent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (FAIRE-seq)
According to current models, transcription factors (TFs) activated by extracellular stimuli operate in the context of a pre-established enhancer repertoire induced and maintained by lineage-specific TFs. Here, we uncovered the existence of latent enhancers, defined as regions of the genome that in t...
ORGANISM(S): Mus musculus 
2013-01-17 | E-GEOD-41677 | biostudies-arrayexpress
GenomicsIllumina_SNParray - samples
SNP array of 7 HCCs and matched background liver in children with bile salt export pump deficiency
EGAD00010000560 | EGA
Genomicsena-DATASET-KCL-CS-01-04-2014-19:21:08:940-7 - samples
Whole exome sequencing of 6 HCCs and matched background liver in children with bile salt export pump deficiency.
EGAD00001000811 | EGA
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