GEO DataSets

(Submitter supplied) Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. We present a computational method, dynamic motif occupancy (DynaMO), which exploits random forest modeling and clustering based enrichment analysis. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

30 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. more...

Organism:

Saccharomyces cerevisiae W303; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

8 Samples

Download data: TXT

(Submitter supplied) The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

16 Samples

Download data: TXT

(Submitter supplied) The wild-type (grown on galactose or glucose) or msn2/4 mutant (grown on galactose) strains were grown aerobically. At time zero (generation 0) the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth. Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS2002 GDS2003

Platform:

GPL1535

45 Samples

Download data

Analysis of catabolite-derepressed (galactose) wildtype JM43 and isogenic msn2/4 mutant KKY8 cells shifted to short-term anaerobiosis (2 generations). Msn2 and 4 are key stress factors. Results suggest Msn2/4 involvement in metabolic remodeling during acclimatization to short-term anaerobiosis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 genotype/variation, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

Download data

Analysis of catabolite-repressed (glucose) or derepressed (galactose) wildtype JM43 cells shifted from aerobiosis to anaerobiosis (2 generations). Results identify metabolic remodeling that occurs during acclimatization to short-term anaerobiosis in galactose but not in glucose.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 growth protocol, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

Download data

(Submitter supplied) The response to proteotoxic stresses such as heat shock is an ancient and ubiquitous transcriptional program allowing organisms to maintain protein homeostasis under changing environmental conditions. We depleted or deleted the three stress-specific transcription factors, Hsf1, Msn2 and Msn4, in S. cerevisiae and determined the effects on the transcriptome and proteome. Msn2/4 are responsible for a broad transcriptional reprogramming which includes i. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18085

60 Samples

Download data: TSV, TXT

(Submitter supplied) Cells missing the InsP7 phosphatase Siw14 were exposed to osmotic and oxidative stress and the transcriptional response compared to that in a wild-type strain. The data show that the Siw14 delete strain has an elevated stress reponse in log growth conditions, but still mounts a robust response to acute stress.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

5 Samples

Download data: GPR

(Submitter supplied) Exposure of Saccharomyces cerevisiae to alkaline pH represents a stress condition that generates a compensatory reaction. Here we examine a possible role of the protein kinase-A (PKA) pathway in this response. The phenotypic analysis reveals that mutations that activate the PKA pathway (ira1 ira2, bcy1) tend to cause sensitivity to alkaline pH, whereas its deactivation develops tolerance to this stress. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10039

16 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of Saccharomyces cerevisiae cells comparing the W303-1A wildtype with the W303-1A double mutant for MSN2 and MSN4 during zinc deficient conditions Keywords: Genetic modification with zinc limitation

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL6890

6 Samples

Download data: TXT

(Submitter supplied) Recent single-cell studies have revealed that yeast stress response involves multiple transcription factors that are temporally activated in pulses. However, it remains largely unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. more...

Organism:

Nakaseomyces glabratus; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29410 GPL26171

36 Samples

Download data: CSV

(Submitter supplied) To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7542

6 Samples

Download data: GPR

(Submitter supplied) Msn2 is a transcription factor required for integration of environmental and metabolic signals. Msn2 is directly regulated by the carbon source sensing PKA and AMP pathways. Here we analyse the role of Msn2 for metabolic adjustment by using point mutants mimicking the dephosphorylated state.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

4 Samples

Download data: TXT

(Submitter supplied) To explore the cellular functions of Mhy1, how Mhy1 promotes filamentation, we wanted to identify genes that are transcriptionally controlled by Mhy1. To this end, RNA-Seq analysis was conducted in cells of wild-type strain, mhy1Δ mutant and wild-type strain overexpressing MHY1 grown in filament-inducing YNDC7 medium.

Organism:

Yarrowia lipolytica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21780

3 Samples

Download data: TXT

(Submitter supplied) Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo. However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: BED

(Submitter supplied) The yeast proteins Pkh1 and Pkh2 are functional counterparts of the mammalian 3-phosphoinositide-dependent protein kinase 1 (PDK1). Cells carrying simultaneous deletion in both genes, PKH1 and PKH2 are not viable, at least in some genetic backgrounds (Casamayor et al., 1999; Inagaki et al., 1999). Consequently, a different strategy is needed to study the function of these apparently redundant gene products. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10039

4 Samples

Download data: GPR

(Submitter supplied) The yeast proteins Pkh1 and Pkh2 are functional counterparts of the mammalian 3-phosphoinositide-dependent protein kinase 1 (PDK1). Cells carrying simultaneous deletion in both genes, PKH1 and PKH2 are not viable, at least in some genetic backgrounds (Casamayor et al., 1999; Inagaki et al., 1999). Consequently, a different strategy is needed to study the function of these apparently redundant gene products. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10039

8 Samples

Download data: GPR

(Submitter supplied) Time course transcription profiling of S. cerevisiae in response to different dynamics of protein kinase A inhibition

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10786

56 Samples

Download data: GPR

(Submitter supplied) The goal of this study was discover the transcription binding synthax for the key differentiation TFs in mouse embryonic stem cells. Genes are regulated through enhancer sequences, in which transcription factor binding motifs and their specific arrangements (syntax) form a cis-regulatory code. To understand the relationship between motif syntax and transcription factor binding, we train a deep learning model that uses DNA sequence to predict base-resolution binding profiles of four pluripotency transcription factors Oct4, Sox2, Nanog, and Klf4. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247 GPL13112

18 Samples

Download data: BED, BIGWIG, BW, NARROWPEAK

(Submitter supplied) This dataset uses DNase-seq to profile the genome-wide DNase I hypersensitivity of mES and mES-derived cells along an early pancreatic lineage and provides the locations of putative Transcription Factor (TF) binding sites using the PIQ algorithm. DNase-seq takes advantage of the preferential cutting of DNase I in open chromatin and steric blockage of of DNase I by tightly bound TFs that protect associated genomic DNA sequences. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT