GEO DataSets

(Submitter supplied) 1. Comparison of Leu3 binding in vitro and in vivo 2. comparison of nucleosome occupancy between with Leu3-binding and without Leu3-binding This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

5 related Platforms

44 Samples

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(Submitter supplied) To compare nucleosome distribution between Leu3-overexpressing and Leu3-binding deficient yeast strains Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4279

12 Samples

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(Submitter supplied) Detect Leu3 targets in S. cerevisiae. Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4273 GPL4278 GPL2506

7 Samples

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(Submitter supplied) DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tiling arrays to identify the consensus sequence for each transcription factor as a whole in the genome.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7699

14 Samples

Download data: GFF, PAIR, TIFF

(Submitter supplied) Nucleosome organization is critical for gene regulation. In living cells, this organization is determined by multiple factors, including the action of chromatin remodelers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. more...

Organism:

Homo sapiens; Mus musculus; synthetic construct; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9423 GPL9377 GPL7641

8 Samples

Download data: TAB, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9529 GPL13965

40 Samples

Download data: FTR, MAP

(Submitter supplied) Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide to reveal new relationships between regulators of stress-dependent gene expression.

Organism:

Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13965

6 Samples

Download data: MAP

(Submitter supplied) Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast.

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL9529

22 Samples

Download data: FTR

(Submitter supplied) Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide. and reveal new relationships between regulators of stress-dependent gene expression in yeast.

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9529

6 Samples

Download data: FTR

(Submitter supplied) Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9529

6 Samples

Download data: FTR

(Submitter supplied) Precise gene expression patterns are established by timely and specific binding of transcription factors (TFs) to regulatory sequences. While these events occur in the context of chromatin, our understanding of how TF-nucleosome interplay affects gene expression is highly limited. Here we present a novel assay for high-resolution measurements of both DNA occupancy and gene expression on large-scale libraries of systematically designed regulatory sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL17143

2 Samples

Download data: XLSX

(Submitter supplied) Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) B296bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: TXT

(Submitter supplied) Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

4 Samples

Download data: TXT

(Submitter supplied) Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

9 Samples

Download data: WIG

(Submitter supplied) Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL7250 GPL7542

15 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7542

8 Samples

Download data: TXT

(Submitter supplied) The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

7 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that Rap1, a master regulator of yeast metabolism, binds to an expanded target set upon nutrient depletion despite decreasing protein levels and no evidence of posttranslational modification. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4414

106 Samples

Download data: GPR

(Submitter supplied) We generated S.cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors were replaced with the K.lactis copies. With this candidate approach, we found that K.lactis Chd1 directed longer nucleosome repeat length in S.cerevisiae. Generating chimeric proteins revealed that the strongest contribution to this differential spacing lies in the undercharacterised N-terminus of Chd1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL13272 GPL17143

22 Samples

Download data: TXT