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TranscriptomicsiRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
RNA-seq is a sensitive and accurate technique to compare steady state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we ha...
ORGANISM(S): Homo sapiens 
2015-02-04 | E-GEOD-60462 | biostudies-arrayexpress
TranscriptomicsTranscription factor cooperativity in early adipogenic hotspots and super-enhancers
Here we have used a combination of advanced proteomics and genomics approaches to investigate the extent and mechanisms of transcription factor cross-talk at genomic hotspots. We identify ~12,000 transcription factor hotspots in the early phase of adipogenesis, and we find evidence of both simultane...
ORGANISM(S): Mus musculus 
2014-04-17 | E-GEOD-56872 | biostudies-arrayexpress
GenomicsAcute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers
The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose tissue inflammation and development of insulin resistance during obesity. In this context, nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB), is directly involved and required for t...
ORGANISM(S): Homo sapiens 
2015-06-17 | E-GEOD-64233 | biostudies-arrayexpress
TranscriptomicsMolecular architecture of transcription factor hotspots in early adipogenesis
Here, we have used digital genomic footprinting to precisely define protein localization for several adipogenic transcription factors at a genome-wide level. In combination with ChIP-seq data, these analyses reveal novel molecular insight into the organization of transcription factors at hotpot regi...
ORGANISM(S): Mus musculus 
2014-05-08 | E-GEOD-57415 | biostudies-arrayexpress
GenomicsExtensive Chromatin Remodeling and Establishment of Transcription Factor 'Hotspots' during Early Adipogenesis
Adipogenesis is tightly controlled by a complex network of transcription factors acting at different stages of differentiation. Peroxisome proliferator-activated receptor gamma (PPAR gamma) and CCAAT/enhancer binding protein (C/EBP) family members are key regulators of this process. We have employ...
ORGANISM(S): Mus musculus 
2011-03-22 | E-GEOD-27826 | biostudies-arrayexpress
GenomicsCross-species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites
We used chromatin immunoprecipitation combined with deep sequencing to map all binding sites of C/EBPα and PPARγ in human SGBS adipocytes and compared these with the genome-wide profiles from mouse 3T3-L1 adipocytes to systematically investigate what biological features correlate with retention of s...
ORGANISM(S): Homo sapiens 
2011-02-23 | E-GEOD-27450 | biostudies-arrayexpress
GenomicsGenome-wide profiling of PPAR?:RXR and RNA polymerase II
Genome-wide profiling of PPAR?:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis. Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activat...
ORGANISM(S): Mus musculus 
2008-12-10 | E-GEOD-13511 | biostudies-arrayexpress
GenomicsGenome-Wide Profiling of Peroxisome Proliferator-Activated Receptor M-NM-3 in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression
Here we have employed chromatin immunoprecipitation combined with deep sequencing to map and compare PPARM-NM-3 binding in in vitro differentiated primary mouse adipocytes isolated from epididymal, inguinal, and brown adipose tissues. While these PPARM-NM-3 binding profiles are overall similar, the...
ORGANISM(S): Mus musculus 
2012-10-11 | E-GEOD-41481 | biostudies-arrayexpress
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