GEO DataSets

(Submitter supplied) Cells are subjected to dramatic changes on gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. Genome wide localisation studies showed major changes on Pol II localisation towards stress-responsive genes in contrast to housekeeping genes. Pol II relocalisation requires of the Hog1 SAPK, which also associates at stress-responsive loci. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

15 Samples

Download data: BED

(Submitter supplied) Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling Keyword: genetic modification

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7542

3 Samples

Download data: GPR

(Submitter supplied) When challenged with osmotic shock, S. cerevisiae induces hundreds of genes, despite a global reduction in transcriptional capacity. The mechanisms that regulate this rapid reallocation of transcriptional resources are not known. Here we show that redistribution of RNA Pol II upon stress requires the stress-responsive MAP kinase Hog1. We find that Hog1 and RNA Pol II co-localize to open reading frames that bypass global transcriptional repression, and that these targets are specified by two osmotic stress-responsive transcription factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

18 Samples

Download data: TXT

(Submitter supplied) To study the relevance of the phosphorylation of Spt4 in residues T42 and S43, we assessed the genome-wide transcriptional response of the non-phosphorylatable Spt4-T42A/S43A mutant (Spt4-AA) upon osmotic stress. Results point out that the unphosphorylatable Spt4-T42A/S43A protein showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in osmotic stress responsive transcriptional regulation.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TSV

(Submitter supplied) We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion and swi3 (component of SWI/SNF complex involved in chromatin remodeling) deletion in genes involved in cell wall stress (Congo Red) response.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

18 Samples

Download data: CEL

(Submitter supplied) Using pol II mutants in human cells we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; H3K36me3 shifted within genes toward 5’ ends and H3K4me2 extended further upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5’ ends of genes that is conserved in yeast. We propose a “dwell-time in the target zone” model to explain the effects of transcriptional dynamics on establishment of co-transcriptionally deposited protein modifications. more...

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

53 Samples

Download data: BW, TDF

(Submitter supplied) Expression microarrays of WT vs. hog1D cells in aerobic or 5 hours of hypoxic growth (100% nitrogen gas).

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Expression profiling by array

Platform:

GPL11382

6 Samples

Download data: TXT

(Submitter supplied) Yeast Hog1-3HA ChIP-Chip in triplicate Keywords: ChIP-Chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1689

3 Samples

Download data

(Submitter supplied) This study was performed to characterize the gene expression profile of rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). Keywords: Rat, Mesotheliomas, Bromochloractetic acid, o-Nitrotoluene, Carcinogenesis, Microarray

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS2051

Platform:

GPL890

16 Samples

Download data: TIFF, TXT

Analysis of peritoneal mesotheliomas induced by various concentrations of o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). o-NT is a high production chemical. BCA is a by-product of drinking water disinfection. Results provide insight into the mechanisms underlying mesothelioma formation.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, log10 ratio, 2 agent, 5 dose sets

Platform:

GPL890

Series:

GSE4682

16 Samples

Download data: TIFF, TXT

(Submitter supplied) We examine how SUMO post-translational modification of the yeast transcription factor Sko1 affects its binding site selection and affinity. Chromatin immunoprecipitation followed by next-generation sequencing was performed in strains expressing wild-type Sko1 (Sko1-WT) or Sko1 that harbors an Arg-to-Lys mutation at Lys 567 (Sko1-MT), that impairs its sumoylation. We find that, compared with Sko1-WT, SUMO-deficient Sko1 binds numerous additional sites that are near promoters of non-Sko1 target genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TXT

(Submitter supplied) It is unclear how the amount of active nuclear MAPK over time quantitatively affects transcription. Here, we seek to address this issue by studying signal transduction and transcriptional response in a system that separates signalling from adaptation and hence signal strength from signal duration. The system is based on Saccharomyces cerevisiae osmoadaptation and allows modulation of the period of HOG-dependent responses without changing the initial stress intensity. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4462

16 Samples

Download data: TXT

(Submitter supplied) The packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is associated with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here that antisense RNA Polymerase II (Pol II) transcription is critical to prime and maintain nucleosome depletion at Pol III loci and allow efficient Pol III recruitment upon re-initiation of growth from stationary phase. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL17225

12 Samples

Download data: BW, TXT

(Submitter supplied) Epigenetic information is able to interact with the cellular environment and therefore it could be especially useful for reprogramming gene expression in response to a physiological perturbation. In fact, genes induced or repressed by osmotic stress undergo significant changes in the levels of various histone modifications, especially the acetylation levels of histone H3. Exposure of yeast to high osmolarity results in the activation of p38-related SAPK, Hog1, which plays a central role in the control of gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4130

4 Samples

Download data: TXT, XLSX

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

58 Samples

Download data: TAB

(Submitter supplied) Gene expression was quantified in crz1 hog1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. We show that calcineurin-dependent downregulation of G1/S genes is partly dependent on the osmostress-activated kinase Hog1.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

16 Samples

Download data: TXT

(Submitter supplied) Gene expression was quantified in crz1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. A strain with a calcineurin-resistant mutation in the transcription factor Hcm1 was also examined. We show that calcineurin activation leads to downregulation of a many clusters of cell cycle-regulated genes, including those expressed at the G1/S and G2/M transitions.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

42 Samples

Download data: TAB

(Submitter supplied) We report gene expression patterns and chromatin architecture changes as yeast re-enter the cell cycle from quiescence

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

49 Samples

Download data: BW

(Submitter supplied) The goal of the project was to study the response in transcription rates after 0.6M KCl addition genome wide. We used Genomic Run-On (GRO) experiment taking samples at 0, 8, 15, 30, and 45 minutes after salt addition in wild type and xrn1 mutant strains.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24365

10 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10930 GPL7250

62 Samples

Download data: BAR, CEL, TXT