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TranscriptomicsAnalysis of nucleosome occupancy in yeast using a whole genome tiling array
Nucleosomal DNA and whole genomic DNA from Saccharomyces cerevisiae BY4741 were isolated and hybridized to the yeast whole genome tiling array. Cells were grown in rich medium (YPD) to mid-log phase.
ORGANISM(S): Saccharomyces cerevisiae 
2007-09-16 | E-MEXP-1172 | biostudies-arrayexpress
GenomicsNucleosome positioning for 4 yeast species
We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a prono...
ORGANISM(S): Saccharomyces cerevisiae 
2011-12-09 | E-GEOD-23577 | biostudies-arrayexpress
TranscriptomicsAbf1 and Rap1 effect on nucleosome occupancy in yeast
We grew wild type and corresponding mutant abf1 and rap1 temperature sensitive yeast at 25 C, then for one hour after shifting to 37 C. We then prepared nucleosomal (mostly mononucleosomal) DNA and hybridized to tiling arrays. Three abf1 ts mutant and corresponding wild type, and three rap1 ts muta...
ORGANISM(S): Saccharomyces cerevisiae 
2010-10-15 | E-GEOD-22514 | biostudies-arrayexpress
GenomicsA compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [Nuc-Seq]
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-22 | E-GEOD-44878 | biostudies-arrayexpress
TranscriptomicsA compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [nucleosome profiling]
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-22 | E-GEOD-44877 | biostudies-arrayexpress
TranscriptomicsA compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-22 | E-GEOD-44879 | biostudies-arrayexpress
TranscriptomicsA compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [transcript profiling]
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-22 | E-GEOD-44876 | biostudies-arrayexpress
GenomicsNucleosome repositioning-coupled expression divergence between species
We describe the genome-wide nucleosome profiles for S. bayanus under standard conditions Nucleosomes from S. bayanus was isolated and sequenced using the Illumina GAII platform.
ORGANISM(S): Saccharomyces bayanus 
2011-11-10 | E-GEOD-24356 | biostudies-arrayexpress
Transcriptomics293_hORF3.1_drug_treatments_partII
Overexpression of the transcription factor RHOXF2 in the HEK293_M2 cells confers resistance to several DNA damaging agents. To understand that resistance mechanism, we cultured HEK293_M2 with or without overexpression of RHOXF2 in the presence of 40nM of mitomycin C or DMSO (control) and profiled th...
ORGANISM(S): Homo sapiens 
2014-05-15 | E-MTAB-2497 | biostudies-arrayexpress
TranscriptomicsA Signaling Lipid Associated with Alzheimer’s Disease Promotes Mitochondrial Dysfunction
Fundamental changes in the composition and distribution of lipids within the brain are believed to contribute to the cognitive decline associated with Alzheimer’s disease (AD). The mechanisms by which these changes in lipid composition affect cellular function and ultimately cognition are not well...
ORGANISM(S): Saccharomyces cerevisiae 
2016-01-21 | E-GEOD-40814 | biostudies-arrayexpress
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