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TranscriptomicsComparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.
Topological domains are key architectural building blocks of chromosomes in complex genomes. Their functional importance and evolutionary dynamics are however not well defined. Here we performed comparative Hi-C in liver cells from four mammalian species, and characterized the conservation and dive...
ORGANISM(S): Canis lupus familiaris 
2015-02-26 | E-GEOD-65126 | biostudies-arrayexpress
TranscriptomicsDifferential production of Type I IFN determines the reciprocal levels of IL-10 and proinflammatory cytokines produced by C57BL/6 and BALB/c macrophages
Pattern recognition receptors (PRR) detect microbial products and induce cytokines which shape the immunological response. Interleukin-12 (IL-12), tumor necrosis factor alpha (TNF-α) and IL-1β are proinflammatory cytokines which can be essential for resistance against infection, but if produced at...
ORGANISM(S): Mus musculus 
2016-09-07 | E-GEOD-79809 | biostudies-arrayexpress
TranscriptomicsChIP-chip analysis of HTZ-1 and RNA Polymerase II in wildtype (N2) embryos
In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for viability in all metazoans tested to date. However, the function of H2A.Z in chromatin organiza...
ORGANISM(S): Caenorhabditis elegans 
2010-05-25 | E-GEOD-10201 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human age-dichotomized ER+, N0 breast tumors reveals enhanced NF kappa B and AP-1 activity associated with antiestrogen resistant breast caner
Signaling pathways that converge on two different transcription factor complexes, NFκB and AP-1, have been identified in estrogen receptor (ER)-positive breast cancers resistant to the antiestrogen, tamoxifen. In this study, biomarkers co-ordinately up-regulated by NFKB and AP-1 with prognositic si...
ORGANISM(S): Homo sapiens 
2008-06-15 | E-GEOD-7378 | biostudies-arrayexpress
TranscriptomicsNS1-mediated inhibition of c-Abl results in acute lung injury and priming for bacterial co-infections; insights into 1918 H1N1 pandemic
NS1 proteins from avian influenza viruses like the 1918 pandemic NS1 are capable of inhibiting the key signaling integrator c-Abl (Abl1), resulting in massive cytopathic cell alterations. In the current study, we addressed the consequences of NS1-mediated alteration of c-Abl on acute lung injury and...
ORGANISM(S): Mus musculus 
2014-11-03 | E-GEOD-62169 | biostudies-arrayexpress
TranscriptomicsDeep sequencing the circadian and light-dependent transcriptome of Drosophila brain
Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-hour rhythms of transcription.These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over th...
ORGANISM(S): Drosophila melanogaster 
2012-03-27 | E-GEOD-36108 | biostudies-arrayexpress
TranscriptomicsPolypyrimidine tract-binding protein homologues from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes
Alternative splicing (AS) generates transcript variants by the definition of different exonic and intronic regions and causes a massive expansion of transcriptome diversity. Changes in AS patterns have been found to be linked to manifold biological processes, yet fundamental aspects such as the regu...
ORGANISM(S): Arabidopsis thaliana 
2012-10-22 | E-GEOD-41433 | biostudies-arrayexpress
MetabolomicsIntegrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency
Functional oncogenic links between ErbB2 and ERRα in HER2+ breast cancer patients support a therapeutic benefit of co-targeted therapies. However, ErbB2 and ERRα also play key roles in heart physiology, and this approach could pose a potential liability to cardiovascular health. Herein, using integr...
2022-09-20 | MTBLS795 | MetaboLights
ProteomicsA tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling
Pseudomonas aeruginosa is a difficult-to-treat Gram-negative bacterial pathogen causing life-threatening infections. Adaptive resistance (AR) to cationic peptide antibiotics such as polymyxin B impairs the therapeutic success. This self-protection is mediated by two component systems consisting of a...
ORGANISM(S): Pseudomonas Aeruginosa Pao1 
2021-08-19 | PXD022470 | panorama
MetabolomicsThe phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 inhibitor 3PO is a modulator of neutrophil metabolism, ROS production and NET release
Neutrophils are key effector leukocytes of the innate immune system and play a pivotal role in defending the host against microbial infections. Recent studies have identified a crucial link between glycolysis and neutrophil cellular functions. We have investigated in human neutrophils, the intricate...
2025-08-14 | MTBLS6215 | MetaboLights
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