GEO DataSets

(Submitter supplied) Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: CSV, XLSX

(Submitter supplied) Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

8 Samples

Download data: BW

(Submitter supplied) The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. more...

Organism:

Populus tremula x Populus alba

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34368

7 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Toxoplasma gondii persists in humans by converting from actively replicating acute stage tachyzoites to slow-growing chronic stage bradyzoites. The molecular mechanisms that mediate T. gondii differentiation remain poorly understood. Through a chemical mutagenesis screen, we identified translation initiation factor eIF1.2 as being critical for T. gondii differentiation. The presence of an F97L mutation in eIF1.2 identified in the screen or the complete lack eIF1.2 (∆eIF1.2) markedly impeded bradyzoite cyst formation in culture and in the brains of infected mice. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23466

24 Samples

Download data: TXT

(Submitter supplied) Proper mitochondrial function is critical for the ability of the fungal pathogen Cryptococcus neoformans to cause disease. Mitochondrial dysfunction of WT cells treated with antimycin A or L-DOPA, or on cells lacking Cir1 is evident from this dataset. These experiments revealed influences on transcript levels of genes encoding Fe-S cluster assembly components and the response to oxidative stress in Cryptococcus neoformans.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24579

15 Samples

Download data: TXT

(Submitter supplied) TREX (transcription and export) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and metazoan CIP29/SARNP. Using biochemical approaches, the domains of MOS11 required for interaction with UAP56 and RNA-binding were identified. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30821

28 Samples

Download data: TSV

(Submitter supplied) tRNA modifications play important roles in maintaining translation accuracy in all domains of life. Disruptions in the tRNA modification machinery, especially of the anticodon stem loop, can be lethal for many bacteria and lead to a broad range of phenotypes in baker’s yeast. Very little is known about the function of tRNA modifications in host-pathogen interactions, where rapidly changing environments and stresses require fast adaptations. more...

Organism:

Candida albicans

Type:

Other

Platform:

GPL22403

12 Samples

Download data: TXT

(Submitter supplied) Pathogens have to cope with oxidative, iron- and carbon-limitation stresses in the human body. To understand how combined iron-carbon limitation alters oxidative stress response, Aspergillus fumigatus was cultured in glucose-peptone or peptone containing media supplemented or not with deferiprone as iron chelator. Changes in the transcriptome in these cultures were recorded after H2O2 treatment. Responses to oxidative stress were highly dependent on the availability of glucose and iron. more...

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23268

24 Samples

Download data: XLSX

(Submitter supplied) Work summary: Full-transcriptome methods have brought versatile power to protein biosynthesis research, but remain difficult to apply for the quantification of absolute protein synthesis rates. Here we propose and, using modified translation complex profiling, confirm co-localisation of ribosomes on messenger(m)RNA resulting from the ribosomal diffusional dynamics. We demonstrate that the stochastically co-localised ribosomes are linked with the translation initiation rate and provide a robust variable to model and quantify specific absolute protein output from mRNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

18 Samples

Download data: BED

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

60 Samples

Download data

(Submitter supplied) Gene expression was quantified in S. cerevisae cells after 48 hours of treatment with KCl. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We find that calcineurin has very little effect on gene expression in response to KCl.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

12 Samples

Download data: CSV

(Submitter supplied) Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We show that mitochondrial genes are downregulated in both geneotypes over time. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

24 Samples

Download data: CSV

(Submitter supplied) Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. Wild type (WT) and cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes. We show that mitochondrial genes are downregulated, and ribosome biogenesis genes are upregulated, in both geneotypes over time.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

24 Samples

Download data: CSV

(Submitter supplied) Bacteria rely on DNA methylation for restriction modification systems and for epigenetic control of gene expression. In Alphaproteobacteria, the CcrM orphan methyltransferase is particularly noteworthy in a range of transcriptional regulation. The wider adoption of nanopore sequencing and updated processing pipelines has made epigenome measurements in bacteria more convenient than before. Here, we validate this approach in Alphaproteobacteria by measuring CcrM-dependent DNA methylation in Caulobacter crescentus and show excellent correlation with other approaches. more...

Organism:

Brucella abortus 2308; Caulobacter vibrioides NA1000

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL34272 GPL34273

10 Samples

Download data: TSV

(Submitter supplied) Maintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allowed us to infer their evolutionary conservation and divergence across these lineages. more...

Organism:

Chlamydomonas reinhardtii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34271

45 Samples

Download data: TXT

(Submitter supplied) We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in response to four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate, Phleomycin.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

4 Samples

Download data: TXT

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

6 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

58 Samples

Download data: WIG

(Submitter supplied) RNA-seq analysis of wild type prototrophic Streptomyces coelicolor A3(2) MT1110 strain to examine global transcriptional profile change when exposed to cold shock from 30°C to 10°C in rich liquid medium, minimal solid medium and in minimal liquid medium

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26763

36 Samples

Download data: CSV, TSV

(Submitter supplied) RNA-seq analysis of wild type Streptomyces coelicolor A3(2) MT1110 to examine global transcriptional profile change when exposed to cold shock from 30°C to 10°C in rich liquid medium and from 30°C to 4°C on minimal solid medium.

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26763

24 Samples

Download data: TSV