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GenomicsPromoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq
Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription ...
ORGANISM(S): Mus musculus 
2010-04-02 | E-GEOD-20530 | biostudies-arrayexpress
GenomicsInterplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana
DNA methylation is an epigenetic mark that is associated with transcriptional repression of transposable elements and protein coding genes. Conversely, transcriptionally active regulatory regions are strongly correlated with histone 3 lysine 4 di- and trimethylation (H3K4m2/3). We previously showed ...
ORGANISM(S): Arabidopsis thaliana 
2013-11-01 | E-GEOD-49090 | biostudies-arrayexpress
MetabolomicsSex-specific effects of CD248 on metabolism and the adipose tissue lipidome

Cd248 has recently been associated with adipose tissue physiology, demonstrated by reduced weight gain in high fat diet-fed mice with genetic deletion of Cd248 relative to controls. Here we set out to determine the metabolic consequences of loss of Cd248. Strikingly, we find these to be sex speci...

2023-01-05 | MTBLS6615 | MetaboLights
GenomicsGenome wide binding of ATF4 and CEBPG bZIP transcription factors in MEFs under amino acid deprived (AAD) conditions
The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances and ER stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) toget...
ORGANISM(S): Mus musculus 
2015-11-19 | E-GEOD-75165 | biostudies-arrayexpress
TranscriptomicsGene profiling of TRA1 and tra1-L3733A
Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase kinase family that contain a C-terminal PI3K domain followed by a 35-residue FATC domain. We analyzed alleles with single residue changes in the FATC domain. Of these tra1-L3...
ORGANISM(S): Saccharomyces cerevisiae 
2010-09-19 | E-GEOD-18591 | biostudies-arrayexpress
TranscriptomicsPronounced and Extensive Microtubule Defects in a Saccharomyces cerevisiae DIS3 Mutant
The recently proposed exozyme hypothesis posits that subunits of the RNA processing exosome assemble into structurally distinct protein complexes that function in disparate cellular compartments and RNA metabolic pathways. Here, in a genetic test of this hypothesis, we examine the role of Dis3 -- a...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-01 | E-GEOD-29018 | biostudies-arrayexpress
GenomicsChromatin immunoprecipitation with next generation sequencing (ChIP-seq) of H3K27ac in primary human macrophages and foam cells
We report the enhancer landscape in primary human macrophages and foam cells using ChIP-seq for the H3K27ac histone mark CD14+ monocytes were isolated from the blood of 2 healthy male volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stim...
ORGANISM(S): Homo sapiens 
2015-04-08 | E-GEOD-54972 | biostudies-arrayexpress
TranscriptomicsmRNA Sequencing of skeletal muscle genes in wildtype and BCATm (BCAT2) KO mice
Consumption of a protein containing meal by a fasted animal promotes protein accretion in skeletal muscle, in part through leucine stimulation of protein synthesis and indirectly through repression of protein degradation mediated by its metabolite, α-ketoisocaproate. Mice lacking the mitochondrial ...
ORGANISM(S): Mus musculus 
2015-12-11 | E-GEOD-68915 | biostudies-arrayexpress
UnknownA novel Netrin-1–sensitive mechanism promotes local SNARE-mediated exocytosis during axon branching
Not available
S-JCBD-201311003 | bioimages
TranscriptomicsGenomic expression over batch growth of mupirocin producing strain Pseudomonas synxantha NCIMB10586
The Pseudomonas synxantha strain NCIMB10586 produces the antibiotic mupirocin / Pseudomonic acid A from a 75 kb gene cluster; expression of this is regulated through quorum-sensing. We wished to examine expression of the strain during batch growth, in particular of the mupirocin cluster and any othe...
ORGANISM(S): Pseudomonas synxantha 
2021-06-04 | E-MTAB-10255 | biostudies-arrayexpress
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