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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
TranscriptomicsConditional Essentiality of vicK (walKSpn) Histidine Kinase for Anaerobic Growth of Streptococcus pneumoniae D39
The VicRK two-component system of S. pneumoniae (Pneumococcus) is a member of the essential WalRK (YycFG) family found in low G+C gram positive bacteria. Previously, we showed that phosphorylated VicR response regulator (RR) is essential, because of its strong positive regulation of the pcsB gene, w...
ORGANISM(S): Streptococcus pneumoniae 
2013-01-04 | E-GEOD-19752 | biostudies-arrayexpress
TranscriptomicsIdentification and function of non-coding small RNAs in Streptococcus pneumoniae
We report here an experimental search for small non-coding RNAs in a low GC, gram-positive, human pathogenic bacteria Streptococcus pneumoniae. Based on the bioinformatic analyses by Livny et al. (2006, Nucleic Acids Res. 34:3484-93), we tested 36 candidates by Northern analyses and confirmed the e...
ORGANISM(S): Streptococcus pneumoniae 
2010-05-14 | E-GEOD-14688 | 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
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 [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
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
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
TranscriptomicsCis- and trans-Regulation of Pneumococcal spxB
Pyruvate oxidase encoded by spxB is a major virulence factor in the human respiratory pathogen Streptococcus pneumoniae. During aerobic growth, SpxB synthesizes large amounts of H2O2 and acetyl phosphate, which can serve as a phosphoryl group donor to response regulators and be converted to ATP. Spx...
ORGANISM(S): Streptococcus pneumoniae 
2010-05-26 | E-GEOD-7109 | 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
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