GEO DataSets

(Submitter supplied) Candida glabrata is an important and increasingly common pathogen of humans, particularly in immunocompromised hosts. Despite this, little is known about how this fungus causes disease. Here, we applied RNA sequencing and an in vivo invasive infection model to identify the attributes that allow this organism to infect hosts. Fungal transcriptomes show a dramatic increase in the expression of Fus3 and Kss1, two mitogen-activated protein kinases (MAPKs), during invasive infection. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33483

9 Samples

Download data: TXT

(Submitter supplied) The loss of a single chromosome in a diploid organism halves the dosage of many genes and is usually accompanied by a substantial decrease in fitness. We asked whether this decrease simply reflects the joint damage caused by individual gene dosage deficiencies. We measured the fitness effects of single heterozygous gene deletions in yeast and combined them for each chromosome. This predicted a negative growth rate, i.e. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

4 Samples

Download data: TSV

(Submitter supplied) Increasing antifungal drug resistance is a major concern associated with human fungal pathogens like Aspergillus fumigatus. Genetic mutation and epimutation mechanisms clearly drive resistance, yet the epitranscriptome remains relatively untested. Here, deletion of the A. fumigatus tRNA-modifying isopentenyl transferase ortholog, Mod5, led to altered stress response and unexpected resistance against the antifungal drug 5-fluorocytosine (5-FC). more...

Organism:

Aspergillus fumigatus

Type:

Other

Platform:

GPL34867

6 Samples

Download data: TSV

(Submitter supplied) The loss of a single chromosome in a diploid organism halves the dosage of many genes and is usually accompanied by a substantial decrease in fitness. We asked whether this decrease simply reflects the joint damage caused by individual gene dosage deficiencies. We measured the fitness effects of single heterozygous gene deletions in yeast and combined them for each chromosome. This predicted a negative growth rate, i.e. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

27 Samples

Download data: TSV

(Submitter supplied) Expression of a typical yeast gene results in ~50 3’ mRNA isoforms that are distinguished by the locations of poly(A) sites within the 3’ untranslated regions (3’ UTRs).The location of poly(A) sites with respect to the translational termination codon varies considerably among genes, but it is unknown whether this has any functional significance.Using hierarchical clustering of 3’ UTRs, we identify eight classes ofS. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

2 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Talaromyces sp. F31

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34664

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F51

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34663

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F50

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34662

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F2(2024)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34661

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. C7(2024)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34660

4 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to characterize the role of VelB in Penicillium expansum. For that a null mutant PeΔVelB was generated.

Organism:

Penicillium expansum

Type:

Expression profiling by array

Platform:

GPL28924

20 Samples

Download data: TXT

(Submitter supplied) Filamentous fungi are promising organisms for lignin degradation and mineralization. However, novel lignin-degrading fungal species are underexplored. Here, we isolated a fungal strain of Curvularia clavata that can utilize lignosulfonate as the carbon source and exhibited a relative high laccase activity during growth on lignosulfonate. Comparative transcriptomic analysis of the WT strain grown on glucose and lignosulfonate indicates that lignosulfonate and/or its metabolites have a significant effect on the gene expression profiles of C. more...

Organism:

Curvularia clavata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34958

15 Samples

Download data: TXT

(Submitter supplied) Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27812

16 Samples

Download data: TXT

(Submitter supplied) Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

6 Samples

Download data: CSV

(Submitter supplied) Non-conventional methylotrophic yeast Komagataella phaffii is an important production host in biotechnology and an emerging model organism. In this work, we studied K. phaffii response to nitrogen starvation during cultivation in media with methanol as the sole carbon source. The results were compared with well-established model yeast Saccharomyces cerevisiae. Some of the observed effects of nitrogen starvation in K. more...

Organism:

Komagataella phaffii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27930

6 Samples

Download data: TXT

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32241

12 Samples

Download data: TXT

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...

Organism:

Candida albicans

Type:

Other

Platform:

GPL32241

28 Samples

Download data: TXT

(Submitter supplied) While nuclear pore proteins mediate nucleo-cytoplasmic transport, they can have important roles in other activities such as transcription, chromatin organization, and cell cycle regulation. The fission yeast nuclear pore protein nup211 localizes to the nuclear basket and is essential for cell viability. Nup211 is important for RNA quality control and the nuclear export of polyadenylated RNAs. Interestingly, several nup211 orthologs have also been shown to regulate transcription at the chromatin level. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

6 Samples

Download data: CSV

(Submitter supplied) Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemic C. auris infections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is that C. auris, unlike most Candida species, displays unique skin tropism and can stay on human skin for a prolonged period. more...

Organism:

Candidozyma auris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29671

6 Samples

Download data: TXT

(Submitter supplied) We showed that the introduction of a 81bp DNA segment in phase genes leads to the generation of fuzzier nucleosome arrays, but neither to a significant change in the placement of the +1 and –last nucleosomes, nor to a coordinate sliding of nucleosomes. This suggests that irrespectively of other nucleosomes, the +1 and –last nucleosomes are placed in well-defined regions marked by sequence-dependent intrinsic and extrinsic factors, while the rest of the nucleosomes are placed based on periodicity considerations.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: GFF