GEO DataSets

(Submitter supplied) This experiment was performed to measure differences in pathway-level evolution of cis-regulation between closely related Kluyveromyces species. Sequencing of mRNA as well as DNA was performed in hybrids of Kl. lactis with two other species, Kl. wickerhamii and Kl. marxianus. Cells were grown overnight for DNA sequencing and for 4-8h to an OD600=0.7-1.0 for mRNA sequencing. DNA and mRNA reads were mapped to hybrid genomes, multimapping reads discarded, and allele-specific expression ratio for each gene was calculated after first normalizing mRNA reads to the number of DNA reads for each gene in each species. more...

Organism:

Kluyveromyces lactis x Kluyveromyces marxianus; Kluyveromyces lactis; Kluyveromyces lactis x Kluyveromyces wickerhamii; Kluyveromyces marxianus; Kluyveromyces wickerhamii

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

24 Samples

Download data: TXT

(Submitter supplied) Abf1 and Rap1 are General Regulatory Factors that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing, and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. We have used microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37 C. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS2533 GDS3198

Platform:

GPL90

12 Samples

Download data: CEL

Analysis of temperature sensitive Abf1 mutant cells subjected to a temperature of 37 degrees C to dissociate the mutant protein from its DNA binding sites. Results provide insight into the contribution of this general regulatory factor to transcription genome-wide.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL90

Series:

GSE6073

6 Samples

Download data: CEL

Analysis of temperature sensitive Rap1 mutant cells subjected to a temperature of 37 degrees C to dissociate the mutant protein from its DNA binding sites. Results provide insight into the contribution of this general regulatory factor to transcription genome-wide.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL90

Series:

GSE6073

6 Samples

Download data: CEL

(Submitter supplied) We analyze genome-wide gene expression response of Saccharomyces cerevisiae to sequential reduction of RAP1 levels.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

12 Samples

Download data: XLSX

(Submitter supplied) Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. more...

Organism:

Candida albicans

Type:

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

Platforms:

GPL6475 GPL6474

16 Samples

Download data: TXT

(Submitter supplied) Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL6475

12 Samples

Download data: TXT

(Submitter supplied) Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. more...

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6474

4 Samples

Download data: TXT

(Submitter supplied) DNA binding protein are generally thought to bind specific DNA sequences through selective interactions with DNA bases. However, it is now becoming more widely appreciated that DNA shape, which may not be specified by a unique base sequence, also contributes to site-specific binding. Here we elucidate how DNA sequence and shape confer site specificity on a genomic scale, and relate this to specificity imparted indirectly through occlusion of sequences by the in vivo environment. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL18573 GPL13821

62 Samples

Download data: GFF

(Submitter supplied) Fhl1-9myc ChIP-chip, YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. AND Ifh1-9myc ChIP-chip, cells grown in YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. Keywords = Fhl1 Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL1689

8 Samples

Download data

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

Organism:

Saccharomyces cerevisiae

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21656 GPL17342

49 Samples

Download data: BIGWIG

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. We have identified that the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21656

7 Samples

Download data: BIGWIG

(Submitter supplied) Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

18 Samples

Download data: BIGWIG, TSV

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL10577

4 Samples

Download data: TXT

(Submitter supplied) We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10577

2 Samples

Download data: TXT

(Submitter supplied) We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

2 Samples

Download data: TXT

(Submitter supplied) While changes in both the coding-sequence of transcriptional regulators and in the cis-regulatory sequences recognized by them have been implicated in the evolution of transcriptional circuits, little is known of how they evolve in concert. We describe an evolutionary pathway in fungi where a new transcriptional circuit (a-specific gene repression by Matα2) evolved by coding changes in an ancient master regulator followed millions of years later by cis-regulatory sequence changes in the genes of its future regulon. more...

Organism:

Wickerhamomyces anomalus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26830

12 Samples

Download data: CSV

(Submitter supplied) We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. more...

Organism:

Kluyveromyces lactis

Type:

Expression profiling by array

Platform:

GPL10962

4 Samples

Download data: GPR

(Submitter supplied) We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. more...

Organism:

Lachancea kluyveri

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15758

6 Samples

Download data: GPR