GEO DataSets

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

(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 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 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.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL7070 GPL7249

5 Samples

Download data: BAR, CEL, TXT

(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) Abf1 and Reb1, two general regulatory factors playing roles at promoters and other genome functional sites in budding yeast, were mapped genome-wide by ChIP-sequencing using strains expressing TAP-tagged versions of the proteins. As expected on the basis of previous in silico analysis of promoter regions, we found that these factors are enriched at the promoters of ribosome biogenesis (Ribi) genes, a large regulon of more than 200 genes required for ribosome biosynthesis and assembly, and known to be coordinately regulated in response to nutrient availability and cellular growth rate.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

4 Samples

Download data: BED

(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) The abf1-1 mutant and wild type cells were grown at 30 degrees C in YPAD until OD600 reached 1.0-1.2. The same volume of 42 degrees C preheated YPAD was added for each flask. After 45 min incubation at 36 degrees C, cells were harvested and RNA was isolated. Four repeats of microarray results are in this series. Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1300

4 Samples

Download data

(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) 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) 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) In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL9377

11 Samples

Download data: BW

(Submitter supplied) Array design -Platform: amino-silane coated glass slides (GAPS II, Corning) -S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1695

15 Samples

Download data: TIFF

(Submitter supplied) All Rap1, Sir2, Sir3, Sir4, and mock immunoprecipitation experiments associated with Lieb et al. Nature Genetics, August 2001, Volume 28, Issue 4 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platforms:

GPL2885 GPL49

26 Samples

Download data

(Submitter supplied) The majority of Saccharomyces cerevisiae snoRNA promoters contain an aRCCCTaa sequence motif located at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound in vivo by Tbf1, a telomere-binding protein known to recognize mammalian-like T2AG3 repeats at sub-telomeric regions. Tbf1 has over 100 additional promoter targets, including the TBF1 gene itself. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

2 Samples

Download data: BED, BEDGRAPH, MAP