GEO DataSets

(Submitter supplied) Sclerotinia sclerotiorum, the causal agent of white mould, is a necrotrophic fungal pathogen responsible for extensive crop loss. Current control options rely heavily on the application of chemical fungicides that are becoming less effective and may lead to the development of fungal resistance. In the current study, we used a foliar spray application of boron to protect Brassica napus (canola) from S. more...

Organism:

Brassica napus; Sclerotinia sclerotiorum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34395 GPL29911

18 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis compares gene expression of the snf22∆ and snf22-(D996A-E997A) mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

9 Samples

Download data: XLSX

(Submitter supplied) Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

7 Samples

Download data: BW

(Submitter supplied) Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

16 Samples

Download data: BW

(Submitter supplied) Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2 and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

21 Samples

Download data: BW

(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) Chromatin-based epigenetic memory relies on the accurate distribution of parental histone tetramers to newly replicated DNA strands, serving as templates for chromatin structure duplication. Mcm2, a subunit of the replicative helicase, and the Dpb3/4, subunits of polymerase epsilon, govern parental histone deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

112 Samples

Download data: BW, TAR

(Submitter supplied) Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions – including those that encode truncated protein isoforms – has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. more...

Organism:

Saccharomyces cerevisiae SK1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33179

8 Samples

Download data: TXT

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

Organism:

Nakaseomyces glabratus

Type:

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

Platforms:

GPL33483 GPL33482

24 Samples

Download data: TXT

(Submitter supplied) MNase-sequencing analysis led to identification of 56,637 to 71,823 nucleosomes under RPMI-growth or macrophage-internalized conditions. Mapping of dynamic nucleosomes revealed that 12 to 24% of total nucleosomes were altered in their position, occupancy or fuzziness. Notably, while the nucleosome position shift was the most common dynamic event, the nucleosome fuzziness was the least observed change. more...

Organism:

Nakaseomyces glabratus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33483

8 Samples

Download data: TXT

(Submitter supplied) The goal of the current study was to identify differentially-expressed genes upon CgSNF2 deletion, as well as, upon macrophage internalization in C. glabrata wild-type (wt) and Cgsnf2Δ strains. For this study, RNA samples were collected from RPMI-grown and macrophage-internalized cells of C. glabrata wild-type and Cgsnf2Δ strains at 2 h and 10 h post-infection. Comparative transcriptome analysis shows the differential regulation of 1419 genes in C. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33482

16 Samples

Download data: TXT

(Submitter supplied) Epigenetic mechanisms contribute to gene regulation by altering the accessibility of the chromatin, resulting in transcription factor (TF) and nucleosome occupancy changes throughout the genome. A major challenge is defining and dissecting this complex chromatin-mediated code to model transcriptional regulation and predict gene expression. We address this by employing a factor-agnostic, reverse-genetics approach to capture TF and nucleosome occupancies genome-wide in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae using MNase-seq, totalling nearly 1,000,000 possible mutant-gene interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

201 Samples

Download data: RDS

(Submitter supplied) Candida albicansis the leading cause of life-threatening bloodstream candidiasis, especially among immunocompromised patients. The reversible morphological transition from yeast to hyphal filaments in response to host environmental cues facilitatesC.albicanstissue invasion, immune evasion, and dissemination. Hence, it is widely considered that filamentation represents one of the major virulence properties inC.albicans. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33213

8 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) Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18085

15 Samples

Download data: BW

(Submitter supplied) RNA sequencing evidenced a massive transcriptomic change linked to the onset of PeAfpA production for the wild type strain, which was confirmed in the ΔafpA mutant. We identified two gene expression clusters putatively involved in PeAfpA function, which correspond to genes induced or repressed with the production of PeAfpA.

Organism:

Penicillium expansum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34193

12 Samples

Download data: TXT

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

Organism:

Fusarium fujikuroi

Type:

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

Platform:

GPL33594

25 Samples

Download data: BW