GEO DataSets

(Submitter supplied) Development of MAP-C (mutation analysis in pools by chromosome conformation capture), which involves performing 3C on a pool of mutants (generated by programmed oligonucleotide pools, error-prone PCR, or existing mutant collections), followed by amplification of 3C DNA using primers specific to a chromosomal contact of interest (with the mutagenized or barcode region included), and as a control, amplifying the mutagenized or barcode region regardless of ligation. more...

Organism:

Saccharomyces cerevisiae; synthetic construct; Saccharomyces cerevisiae x Saccharomyces uvarum

Type:

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

5 related Platforms

123 Samples

Download data: BED, BEDGRAPH, FA, GFF, TXT

(Submitter supplied) In the yeast Saccharomyces cerevisiae, certain genomic regions have very high levels of meiotic recombination (hot spots). The hot spot activity associated with the HIS4 gene requires the Bas1p transcription factor. To determine whether this relationship between transcription factor binding and hot spot activity is general, we used DNA microarrays to map all genomic Bas1p binding sites and to map the frequency of meiosis-specific double-strand DNA breaks (as an estimate of the recombination activity) of all genes in both wild-type and bas1 strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4414

11 Samples

Download data: GPR

(Submitter supplied) Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac∆), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes1,2, and recent high-throughput chromatin conformation capture (Hi-C)2 methods have allowed systematic and unbiased measurement of this organization. Using polymer modeling, some groups have suggested that yeast genome conformation is simple and dominated by its Rabl-like orientation (anaphase-like polarization)3,4. more...

Organism:

Saccharomyces cerevisiae x Saccharomyces paradoxus; Saccharomyces paradoxus x Saccharomyces uvarum; Saccharomyces uvarum; Saccharomyces cerevisiae x Saccharomyces uvarum; Saccharomyces cerevisiae; Saccharomyces paradoxus

Type:

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

7 related Platforms

44 Samples

Download data: BED, BEDGRAPH, GFF, TXT

(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:

GPL4278 GPL2506 GPL4273

7 Samples

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(Submitter supplied) Cellular processes are subject to variability, or noise, yet mechanisms that promote cell-to-cell uniformity are poorly understood. We have identified such a role for Dig1, a redundant (with Dig2) MAPK-responsive inhibitor of the S. cerevisiae mating pathway transcription factor Ste12. Cells lacking Dig1, but not Dig2, exhibited increased variability in outputs of the mating pathway. dig1∆ mutants also displayed a Ste12-dependent defect in growth in the absence of mating pheromone and a quantitative defect in the process of mating, itself. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4130

16 Samples

Download data: GPR

(Submitter supplied) Meiotic recombination promotes genetic diversification as well as pairing and segregation of homologous chromosomes, but the double-strand breaks (DSBs) that initiate recombination are dangerous lesions that can cause mutation or meiotic failure. How cells control DSBs to balance between beneficial and deleterious outcomes is not well understood. This study tests the hypothesis that DSB control involves a network of intersecting regulatory circuits. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL17342

4 Samples

Download data: WIG

(Submitter supplied) Eukaryotic transcription activators stimulate the expression of specific sets of target genes through recruitment of co-activators such as the RNA polymerase II-interacting Mediator complex. We previously identified an activator-targeted ~85 amino acid three-helix bundle KIX domain in the human MED15 Mediator subunit that is structurally conserved in Gal11 Mediator subunits in fungi. The Gal11 KIX domain is engaged by pleiotropic drug resistance transcription factor (Pdr1) orthologues, key regulators of the multidrug resistance (MDR) pathway in S. more...

Organism:

Nakaseomyces glabratus; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL21066

24 Samples

Download data: TXT

(Submitter supplied) Expression analysis of BY4716(isogenic to S288c) and a wild isolate collected by R. Mortimer. Each strain was grown in culture 6 independent times and RNA from each culture was isolated. Each of these RNA samples was subjected to a dye-swap pair of arrays (except the "RM11" sample, which only got one array). All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent independent cultures. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS93 GDS94

Platform:

GPL118

23 Samples

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(Submitter supplied) Expression analysis of F1 haploid segregants from a cross between BY4716 (isogenic to S288c) and a wild isolate collected by R. Mortimer. Each segregant sample was subjected to a dye-swap pair of arrays. All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent segregants. All sample titles are of the form S1-S2. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS91 GDS92

Platform:

GPL118

80 Samples

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Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain sets

Platform:

GPL118

Series:

GSE38

11 Samples

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Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain sets

Platform:

GPL118

Series:

GSE38

12 Samples

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Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 7 other sets

Platform:

GPL118

Series:

GSE37

40 Samples

Download data

Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 7 other sets

Platform:

GPL118

Series:

GSE37

40 Samples

Download data

(Submitter supplied) A fundamental problem in biology is the molecular basis for divergence among related organisms. We have investigated the level of divergence of transcription factor binding sites for two key factors that regulate developmental processes in the budding yeasts. The genomic binding locations for the Ste12 and Tec1 transcription factors in S. cerevisiae, S. mikatae and S. bayanus were mapped by chromatin immunoprecipitation combined with microarrays (chIP chip)1, 2 and compared to one another. more...

Organism:

Candida albicans; Saccharomyces mikatae; Saccharomyces cerevisiae; Saccharomyces bayanus

Type:

Genome binding/occupancy profiling by genome tiling array

4 related Platforms

27 Samples

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(Submitter supplied) Mre11–Rad50–Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. It restricts transcription of coding and noncoding DNA independently by a mechanism that does not require the nuclease activity of Mre11. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL21656

29 Samples

Download data: BW, TAB

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

Organism:

Saccharomyces cerevisiae

Type:

Methylation profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21656 GPL7250

62 Samples

Download data: BIGWIG, BW, CEL, WIG

(Submitter supplied) The Mec1 and Rad53 kinases play a central role during acute replication stress in budding yeast. They are also essential for viability in normal growth conditions, but the signal that activates the Mec1–Rad53 pathway in the absence of exogenous insults is currently unknown. Here, we show that this pathway is active at the onset of normal S phase because dNTP levels present in G1 phase are not sufficient to support processive DNA synthesis and impede DNA replication. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21656

57 Samples

Download data: BIGWIG, BW