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TranscriptomicsAn atlas of TNF alpha-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2
Sequencing of 5'ends of RNA molecules from Caco-2 cells +/- TNFa stimulation CAGE library construction from RNA extracted from Caco-2 cells
ORGANISM(S): Homo sapiens 
2014-07-01 | E-GEOD-54074 | biostudies-arrayexpress
TranscriptomicsHuman Nonsense-Mediated RNA Decay Initiates Widely by Endonucleolysis and Targets snoRNA Host Genes
Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous...
ORGANISM(S): Homo sapiens 
2014-11-18 | E-GEOD-57433 | biostudies-arrayexpress
UnknownspliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Not available
S-EPMC3998036 | biostudies-literature
TranscriptomicsComprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq]
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during ve...
ORGANISM(S): Danio rerio 
2011-11-17 | E-GEOD-32898 | biostudies-arrayexpress
UnknownHuman Gene Promoters Are Intrinsically Bidirectional.
Not available
S-EPMC5485825 | biostudies-literature
GenomicsComprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq]
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during ve...
ORGANISM(S): Danio rerio 
2011-11-17 | E-GEOD-32899 | 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
GenomicsAcute Genome-Wide Effects of Rosiglitazone on PPARγ Transcriptional Networks in Adipocytes
Here we report, for the first time, the acute effects of the synthetic PPARγ agonist rosiglitazone on the transcriptional network of PPARγ in adipocytes. Treatment with Rosiglitazone for 1 hour leads to acute transcriptional activation as well as repression of a number of genes as determined by geno...
ORGANISM(S): Mus musculus 
2013-08-01 | E-GEOD-49423 | biostudies-arrayexpress
TranscriptomicsGRO-seq in HeLa cells
Mapping the nascent RNA transcriptome of HeLa cells with GRO-seq Standard GRO-seq assay from two replicates in HeLa cells
ORGANISM(S): Homo sapiens 
2014-10-04 | E-GEOD-62046 | biostudies-arrayexpress
UnknownIdentification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2.
Not available
S-EPMC4263293 | biostudies-literature
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