GEO DataSets

(Submitter supplied) Co-expression networks have recently emerged as a useful approach for updating and improving gene annotation at a near-genome level. This is based on the hypothesis that function can be inferred by delineating transcriptional networks in which a gene of interest is embedded. In this study, we generated a co-expression network for the filamentous cell factory Aspergillus niger from 128 RNA-seq experiments. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32288

8 Samples

Download data: CSV

(Submitter supplied) Organisms are repeatedly exposed to fluctuating environmental and nutritional conditions. Transcriptional memory has been shown to be a mechanism to cope with these fluctuations because it increases the speed and the magnitude of the cellular response to a certain re-occurring condition and therefore optimizes adaptation and fitness in a given environment. We found that genes coding for sterigmatocystin (ST) production in Aspergillus nidulans are activated stronger when cells are repeatedly exposed to nutrient starvation, compared to cells that experience this condition for the first time. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30666

32 Samples

Download data: TXT

(Submitter supplied) Organisms are repeatedly exposed to fluctuating environmental and nutritional conditions. Transcriptional memory has been shown to be a mechanism to cope with these fluctuations because it increases the speed and the magnitude of the cellular response to a certain re-occurring condition and therefore optimizes adaptation and fitness in a given environment. We found that genes coding for sterigmatocystin (ST) production in Aspergillus nidulans are activated stronger when cells are repeatedly exposed to nutrient starvation, compared to cells that experience this condition for the first time. more...

Organism:

Aspergillus nidulans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30666

26 Samples

Download data: BW

(Submitter supplied) Summary taken from our paper “Aspergillus terreus Sectorization: A Morphological Phenomenon Shedding Light on Amphotericin B Resistance Mechanism”: WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. Afterwards, the cultures were subjected to either DMSO (control) or 1 µg/ml AmB treatment for 1 h/4 h. Triplicates of each combination of these factors were made, resulting in a total of 24 samples. more...

Organism:

Aspergillus terreus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34927

24 Samples

Download data: SF

(Submitter supplied) Aspergillus fumigatus transcription factor AtrR is a critical determinant of the azole resistance phenotype of this organism. AtrR positively regulates expression of a range of genes involved in azole resistance including the ATP-binding cassette transporter-encoding locus abcG1 (cdr1B/abcC) as well as the gene that encodes the enzymatic target of azole drugs cyp51A. Homology searches of A. fumigatus AtrR against a range of fungal species identified highly conserved 25 amino acid region in the carboxy-terminus. more...

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23160

21 Samples

Download data: BIGWIG, XLSX

(Submitter supplied) Identification of global target genes that their expression levels are dependent on the AcuK and the AcuM transcription factors from T. marneffei. Results provided information that the AcuK and AcuM are global regulators important for adaptation and defense against harsh environmental conditions, such as the response to iron limitation, utilization of alternative carbon sources, and antioxidation.

Organism:

Talaromyces marneffei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33968

3 Samples

Download data: XLSX

(Submitter supplied) In order to studing molecular mechanism of Raw Starch Digesting Glucoamylase production in Penicillium oxalicum ,we deleted POX01907 and POX08340 and analyzed the co-expression network of POX08340 and POX01907 at transcriptional level.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32390

6 Samples

Download data: TXT

(Submitter supplied) In order to studing molecular mechanism of Raw Starch Digesting Glucoamylase production in Penicillium oxalicum ,we deleted POX01907 and POX08340 and analyzed the co-expression network of POX08340 and POX01907 at transcriptional level.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32390

9 Samples

Download data: TXT

(Submitter supplied) The synthesis mechanisms and function evaluation of selenium(Se)-enriched microorganism remain relatively unexplored. We here report the Se biotransformation by A. oryzae A02. Comparative RNA-Seq analysis revealed the upregulation of functional genes implicated in selenium transformation, activating multiple potential pathways for selenium reduction. The assimilatory and dissimilatory reductions of Se oxyanions engaged numerous parallel and interconnected pathways, manifesting a harmonious equilibrium in overall Se biotransformation in A. more...

Organism:

Aspergillus oryzae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34650

18 Samples

Download data: TXT

(Submitter supplied) In eukaryotes, methylation of histone H3 at lysine 4 (H3K4me) catalyzed by the complex of proteins associated with Set1 (COMPASS) is crucial for the transcriptional regulation of genes and the development of organisms. In Monascus, the functions of COMPASS in establishing H3K4me remain unclear. This study first identified the conserved COMPASS core subunits MpSet1 and MpSwd3 in Monascus purpureus and confirmed their roles in establishing H3K4me2/3. more...

Organism:

Monascus purpureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33885

9 Samples

Download data: TXT

(Submitter supplied) Coccidioides spp.are part of a group ofthermallydimorphic fungal pathogens, which grow asfilamentous cells (hyphae)in the soil and transform to a different morphology upon inhalation into the host.TheCoccidioideshost form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges.Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. more...

Organism:

Coccidioides posadasii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34553

33 Samples

Download data: TXT

(Submitter supplied) Talaromyces marneffei is the third most common infectious pathogen in AIDS patients and leads to the highest death rate in Guangxi, China. The lack of reliable biomarkers is one of the major obstacles in current clinical diagnosis, which largely contributes to this high mortality. Here, we present a study that aimed at identifying diagnostic biomarker candidates through genome-wide prediction and functional annotation of Talaromyces marneffei secreted proteins. more...

Organism:

Talaromyces marneffei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33968

3 Samples

Download data: TXT

(Submitter supplied) The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. more...

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL33056

36 Samples

Download data: CSV

(Submitter supplied) Aspergillus fumigatus is an important human pathogen and a leading fungal killer. This study aimed to determine the tRNA fragment and tRNA half repertoire of A. fumigatus in wild-type conidia and mycelium grown for 24 or 48 hours in liquid culture.

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23268

9 Samples

Download data: CSV

(Submitter supplied) Transcriptome analysis was performed to identify the differentially expressed genes between hapX mutant and reference strains during their growth on maltose

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

4 Samples

Download data: XLS

(Submitter supplied) Aspergillus niger fulfills an important role in nature in nutrient cycling and is a main cell factory for the industrial production of metabolites and enzymes. Inactivation of flbA in A. niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor genes are differentially expressed in ∆flbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34135

9 Samples

Download data: TSV, XLSX

(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) 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) We generated this RNA-seq dataset to investigate the effects of transcription factor ZfpA (aka. AFUA_8G05010 or AFUB_082490) in the gene expression of A. fumigatus strain Af293. One of the major reasons we were interested in investigating ZfpA was because this TF had been identified as highly regulated by the oxylipins (https://pubmed.ncbi.nlm.nih.gov/33056992/). To that end, we collected RNA from spores and the mycelial tissue under three distinct conditions: (a) wild-type ZfpA, (b) ZfpA knocked out, and (c) ZfpA overexpressed. more...

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33056

24 Samples

Download data: CSV, TSV

(Submitter supplied) Generally, A. niger undergoes two steps consisting of seed stage and fermentation stage to synthesize malic acid. However, it remains unknown which metabolic pathways, regulators, and key genes respond to the transition from seed medium to fermentation medium. In this study, we obtained the total mRMA of a high L-malate-yielding strain A. niger RG0095 at seed stage and fermentation stage, respectively, and performed a global differential expression analysis.

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32288

6 Samples

Download data: TXT