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TranscriptomicsYeast expression data from conditions that inhibit sirtuins
Sir2 is an NAD+-dependent histone deacetylase, and is the founding member of a large, phylogentically conserved, family of such deacetylases called the Sirtuins. The budding yeast, Saccharomyces cerevisiae, harbors 4 paralogs of Sir2, known as Hst1, Hst2, Hst3, and Hst4. Reducing the intracellular N...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-10 | E-GEOD-18488 | biostudies-arrayexpress
TranscriptomicsBubble-seq Analysis of the Human Genome Reveals Distinct Chromatin-Mediated Mechanisms for Regulating Early- and Late-Firing Origins
We have devised a method for isolating virtually pure and comprehensive libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo (Mesner et al. 2009). We have now sequenced and mapped the bubble-containing fragments from GM06990, a near-normal EBV-transformed...
ORGANISM(S): Homo sapiens 
2013-07-09 | E-GEOD-38809 | biostudies-arrayexpress
Transcriptomicschromatin reprogramming and differential gene expression in a model of EMT (spheroid A549 treated with TGF/TNF)
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Homo sapiens 
2013-09-12 | E-GEOD-42375 | biostudies-arrayexpress
TranscriptomicsGene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures
TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when...
ORGANISM(S): Homo sapiens 
2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress
GenomicsHistone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures
We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha. The epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process t...
ORGANISM(S): Homo sapiens 
2013-09-12 | E-GEOD-42374 | biostudies-arrayexpress
GenomicsGenome-wide Analysis of Functional Sirtuin Chromatin Targets in Yeast
Sir2 and the homologous proteins, Hst1, Hst2, Hst3, and Hst4 from Saccharomyces cerevisiae are NAD+-dependent histone deacetylases of the sirtuin protein family. Sir2 functions in transcriptional silencing at the silent mating-type loci, telomeres, and rDNA locus, but also promotes replicative lifes...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-10 | E-GEOD-41415 | biostudies-arrayexpress
TranscriptomicsFunctional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations
The chronological lifespan (CLS) of Saccharomyces cerevisiae is defined as the number days that non-dividing cells remain viable, typically in stationary phase cultures or in water. CLS is extended by restricting glucose in the starting cultures, and is considered a form of caloric restriction (CR)....
ORGANISM(S): Saccharomyces cerevisiae 
2014-09-12 | E-GEOD-61341 | biostudies-arrayexpress
TranscriptomicsThe Mot1 ATPase and Spt16 Histone Chaperone Cooperatively Regulate Transcription
Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaper...
ORGANISM(S): Saccharomyces cerevisiae 
2016-05-16 | E-GEOD-72117 | biostudies-arrayexpress
GenomicsGenome-wide Localization of Mot1, Spt16, and Nucleosomes in mot1, spt16, and mot1 spt16 cells
Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaper...
ORGANISM(S): Saccharomyces cerevisiae 
2016-05-16 | E-GEOD-80234 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of human MCF cells treated with estrogen
The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in b...
ORGANISM(S): Homo sapiens 
2008-06-11 | E-GEOD-11324 | biostudies-arrayexpress
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