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MetabolomicsInositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites
Vesicular traffic and membrane contact sites between organelles enable the exchange of proteins, lipids, and metabolites. Recruitment of membrane tethers to contact sites between the endoplasmic reticulum (ER) and the plasma membrane is often triggered by calcium. In contrast, we reveal here a funct...
2021-05-06 | MTBLS2444 | MetaboLights
TranscriptomicsGenome-Wide STAT5 binding sites in Kit225 leukemia cells
In order to systematically map STAT5 genomic binding sites and IL-2 mediated gene expression changes we mapped STAT5 binding sites using chip-on-ChIP in IL-2 dependent Kit225 cells that were either left un-stimulated or stimulated with IL-2 for 30 minutes. Using MAT analysis we identified 1581 STAT5...
ORGANISM(S): Homo sapiens 
2013-03-21 | E-GEOD-40619 | biostudies-arrayexpress
GenomicsGenome-wide profiling of LXR, RXR and PPARM-NM-1 in mouse liver reveals extensive sharing of binding sites
The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice is dependent on LXR an...
ORGANISM(S): Mus musculus 
2012-01-31 | E-GEOD-35262 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE215...
ORGANISM(S): Homo sapiens 
2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human cell line HEPG2 to identify liver specific transcription factor binding sites
Identification of liver transcription factors binding sites by ChIP-chip using HepG2 cells. Inference of binding sites at base pair resolution was achieved by using bioinformatic tools on the generated data sets.
ORGANISM(S): Homo sapiens 
2005-10-01 | E-MEXP-452 | biostudies-arrayexpress
TranscriptomicsElucidation of Transcriptome-Wide MicroRNA Binding Sites in Human Cardiac Tissues by Ago2 HITS-CLIP
We deciphered Ago2:RNA interactions in post-mortem human heart tissues using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across...
ORGANISM(S): Homo sapiens 
2016-08-09 | E-GEOD-83410 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data
To obtain evidence that Argonaute (AGO) crosslink-centered regions (CCRs) indeed contain functional miRNA-binding sites, we blocked 25 of the most abundant miRNAs in HEK 293 cells (Figure 5C of PMID 20371350) by transfection of a cocktail of 2'-O-methyl-modified antisense oligoribonucleotides and mo...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21577 | biostudies-arrayexpress
TranscriptomicsMapping the inter- and intra-chromosomal interactions of specific insulator binding sites with circular chromosome conformation capture (4C) assay (Gondor et al., 2008 Nature Protocol) [NimbleGen Array data]
Drosophila Insulator proteins mediate long-range chromosomal interactions. ChIP-seq revealed that binding of insulator proteins to some specific DNA sites was regulated by poly(ADP-ribosyl)ation in S2 cells. Three insulator sites regulated by poly(ADP-ribosyl)ation were used as baits to map their di...
ORGANISM(S): Drosophila melanogaster 
2013-09-15 | E-GEOD-50768 | biostudies-arrayexpress
GenomicsHNF4A-binding sites in HepG2 hepatoblastoma cells treated with TGF-beta
Specific regulation of target genes by transforming growth factor-β (TGF-β) in a given cellular context is determined in part by transcription factors and cofactors that interact with the Smad complex. In the present study, we determined Smad2 and Smad3 (Smad2/3) binding regions in the promoters of ...
ORGANISM(S): Homo sapiens 
2011-06-08 | E-GEOD-28845 | biostudies-arrayexpress
GenomicsGenome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes
We use ChIP-seq to discover the genome-wide sites of acetylation of lysine 56 of the histone H3 (H3K56), which is a target of three histone modifying enzymes with known roles in diabetes and insulin resistance, in human adipocytes derived from mesenchymal stem cells. Surprisingly, we find that a ver...
ORGANISM(S): Homo sapiens 
2011-05-31 | E-GEOD-24326 | biostudies-arrayexpress
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