GEO DataSets

Analysis of gene regulation by expression profiling of single mutants for histone deacetylase RPD3, histones H3 and H4, and double mutants for either RPD3 and H3 or RPD3 and H4. Histone mutants defective in amino terminal tails, which are acetylated and deacetylated in transcription regulation.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 8 genotype/variation sets

Platform:

GPL90

Series:

GSE1639

18 Samples

Download data: CEL, EXP

(Submitter supplied) Signal intensity data for rpd3 delete, H3delta(1-28), H3(K4,9,14,18,23,27Q), H4delta(2-26), H4(K5,8,12,16Q), rpd3 delete H3delta(1-28), and rpd3 delete H4(K5,8,12,16Q) yeast grown in rich (YPD) media Keywords = histones Keywords = chromatin Keywords = rpd3 Keywords = HDAC Keywords = histone deacetylase Keywords = yeast Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS772

Platform:

GPL90

18 Samples

Download data: CEL, EXP

(Submitter supplied) Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type Keywords: quadruplicate mutant:WT analysis, with dye-swapping

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3819

8 Samples

Download data: GPR

(Submitter supplied) Histone H2B was mutated to give H2B^3-32, H2B K->G, H2B^3-37, and H2B^30-37. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B HBR domain. This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS2029

Platform:

GPL90

20 Samples

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(Submitter supplied) Histone H2B was mutated to give H2B^30-37. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B HBR domain. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

6 Samples

Download data

(Submitter supplied) Histone H2B was mutated to give H2B^3-37. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal domain. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

6 Samples

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(Submitter supplied) Histone H2B was mutated to give H2B K6,11,16,17,21,22G. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal acetylated lysine residues. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

6 Samples

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(Submitter supplied) Histone H2B was mutated to give H2B^3-32. Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal domain. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

6 Samples

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Analysis of histone H2B mutants that have a substitution of all acetylated N-terminal lysine (K) residues with glycine, or a deletion in the N-terminal domain. Results provide insight into the role of the histone NTD and histone lysine acetylation in transcriptional regulation.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 5 genotype/variation, 6 protocol sets

Platform:

GPL90

Series:

GSE3806

20 Samples

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

70 Samples

Download data: BW, GTF, NARROWPEAK

(Submitter supplied) Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

16 Samples

Download data: BW, GTF

(Submitter supplied) Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

54 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Yeast lacking the H3 or H4 amino termini, and corresponding wild type strains, were grown in synthetic media. These conditions induce Gcn4-activated transcription. Keywords: Genetic modification

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1674

Platform:

GPL90

14 Samples

Download data: CEL, EXP

Expression profiling of H3 and H4 amino terminal deletion mutants grown under conditions of amino acid starvation, which induce Gcn4p activated transcription. Results provide insight into the contribution of histone amino termini modifications to gene expression.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 4 strain sets

Platform:

GPL90

Series:

GSE4135

14 Samples

Download data: CEL, EXP

(Submitter supplied) A series of yeast carrying K->R mutations in the histone H4 N-terminal tail were profiled by gene expression array in mid-log phase. Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1864

55 Samples

Download data

(Submitter supplied) Evidence suggests that the TAF1 subunit of TFIID is a histone acetyltransferase (HAT) that is functionally redundant with the Gcn5 HAT of the SAGA and ADA complexes. Here we test a number of predictions of this hypothesis by examining the in vivo histone acetylation targets of TAF1 and Gcn5, and re-examining the basis for the reported genome-wide functional redundancy between TAF1 and Gcn5. Our findings do not support a number of basic tenets of the hypothesis, thus bringing into question the physiological presence of any TAF1 HAT function in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1924

8 Samples

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(Submitter supplied) Evidence suggests that the TAF1 subunit of TFIID is a histone acetyltransferase (HAT) that is functionally redundant with the Gcn5 HAT of the SAGA and ADA complexes. Here we test a number of predictions of this hypothesis by examining the in vivo histone acetylation targets of TAF1 and Gcn5, and re-examining the basis for the reported genome-wide functional redundancy between TAF1 and Gcn5. Our findings do not support a number of basic tenets of the hypothesis, thus bringing into question the physiological presence of any TAF1 HAT function in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1220

38 Samples

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(Submitter supplied) In budding yeast, telomeres and the mating type (HM) loci are found in a heterochromatin-like silent structure initiated by Rap1 and extended by the interaction of Sir (Silencing Information Regulator) proteins with histones. Binding data demonstrate that both the H3 and H4 N terminal domains required for silencing in vivo interact directly with Sir3 and Sir4 in vitro. The role of H4 lysine 16 deacetylation is well established in Sir3 protein recruitment, however that of the H3 N terminal tail has remained unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

9 Samples

Download data: BAR, CEL

(Submitter supplied) Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H3 K4,9,14,18,23,27,36,79G mutant. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

4 Samples

Download data: CEL

(Submitter supplied) Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H3 K4,36,79G mutant. Keywords: repeat

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

4 Samples

Download data: CEL