GEO DataSets

(Submitter supplied) Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26664

15 Samples

Download data: FA, TXT

(Submitter supplied) In this study,comparative genomic, transcriptomic and secretomic profilings of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106 were employed to screen for novel regulators for cellulase and xylanase gene expression.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20250

6 Samples

Download data: FA, GFF, XLS

(Submitter supplied) A global co-expression network of cellulase and xylanase genes was identified in P. oxalicum, their transcriptional levels depended on the induction of carbon sources and induction time.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24231

72 Samples

Download data: TXT

(Submitter supplied) RNA-seq was used to compare the responses of Penicillium oxalicum strains to different carbon sources including carbon-starvation, glucose and cellulose. The wild-type strain and transcription facor (ClrB, CreA and AmyR) mutants were studied.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20250

24 Samples

Download data: TXT

(Submitter supplied) Transcriptomic profiling and real-time quantitative reverse transcription-PCR analyses revealed that TP05746 dynamically regulated the expression of genes encoding major PBDEs. Furthermore, in vitro binding experiments confirmed that TP05746 directly bound to the promoter regions of these major enzyme genes. Transcription factors mediated the regulation of plant-biomass-degrading enzyme (PBDE) gene expression in Talaromyces pinophilus.

Organism:

Talaromyces pinophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26713

6 Samples

Download data: FASTA, XLS

(Submitter supplied) Filamentous fungi are one of the primary degraders of plant biomass because of their ability to produce enzymes that break down complex polysaccharides. The production of cellulolytic enzymes in fungi is dependent on transcription factors. In this article, we identified a N. crassa Zn2Cys6 transcription factor Clr5 that regulates the expression of cellulase on cellulose. N. crassa Δclr5 exhibited a significant decrease in secreted proteins (~46%), endo-glucanase (~55%), xylanase (~33%), β-glucosidase (~38%), and exocellulase (~40%) compared with the WT, while transcriptomic analysis revealed that clr5 was essential in cellulase expression. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: XLSX

(Submitter supplied) Transcriptional profiling with next-generation sequencing methods refined our understanding of the N. crassa transcriptional response to cellulose and demonstrated that the newly characterized transcription factors clr-1 and clr-2 were required for the bulk of that response including induction all major cellulase and some major hemicellulase genes.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL15147

26 Samples

Download data: TXT

(Submitter supplied) Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. This gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. more...

Organism:

Coprinopsis cinerea AmutBmut pab1-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32332

7 Samples

Download data: GTF, TSV

(Submitter supplied) The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), and laeA knockout strain (ΔlaeA) in different development phase. The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. more...

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20743

4 Samples

Download data: TXT

(Submitter supplied) In thermophilic fungi, work on the ER stress and UPR signalling is largely unknown,we here identified a new Cys2His2 transcription factor and found its knockout strain with significantly decreased cellulases production on crystalline cellulose.Here, we show that loss-of-function mutations of this regulator resulted in the reduced expression of Mthac-1 via RNA-seq under Avicel and artificial ER-stress.

Organism:

Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27455

18 Samples

Download data: XLSX

(Submitter supplied) To explore the effect of phosphokinase POX07948 on the transcription levels of cellulase-encoding genes and xylanase-encoding genes

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24231

6 Samples

Download data: TXT

(Submitter supplied) Fungal degradation of lignocellulosic biomass requires various (hemi-)cellulases and plays key roles in biological carbon cycle. Although cellulases induction recently described in some saprobic filamentous fungi, regulation of cellulase transcription has not been studied thoroughly. Here, we identified and characterized the novel cellulase regulation factors clr-4 in Neurospora crassa and its ortholog Mtclr-4 in Myceliophthora thermophila. more...

Organism:

Neurospora crassa; Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24572 GPL16164

6 Samples

Download data: XLSX

(Submitter supplied) RNA-seq was used to analyze the effects of absence of PoHtf1.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20250

6 Samples

Download data: XLSX

(Submitter supplied) Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. more...

Organism:

Aspergillus niger; Penicillium chrysogenum; Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

7 related Platforms

30 Samples

Download data: FASTA, TXT

(Submitter supplied) In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and β-galactosidase. Here, we determined the CRE-1 regulon by investigating the transcriptome of a Δcre-1 strain compared to wild type when grown on Avicel versus minimal medium (MM). more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

8 Samples

Download data: GPR, TXT

(Submitter supplied) Purpose: To explore conservation of gene regulation by the transcription factor clr-2/clrB in Neurospora crassa and Aspergillus nidulans Methods: mRNA from wild type and clr-2/clrB mutants were collected after a culture shift from sucrose/glucose to Avicel (crystaline cellulose) or no carbon media Results: We show that N. crassa and A. nidulans have similair global transcriptional responses to Avicel, with several hundred genes showing specific induction, though the induced genes are more specifically targeted at cellulose for N. more...

Organism:

Aspergillus nidulans FGSC A4; Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL16600 GPL15147

22 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Transcriptional profiling with next-generation sequencing methods demonstrated that a Neurospora crassa mutant with the three most highly expressed beta-glucosidase genes deleted had a transcriptional response to cellobiose similair to that of wild type N. crassa exposed to cellulose.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15147 GPL15146

13 Samples

Download data: TXT

(Submitter supplied) Purpose: To explore the function of VIB1 in regulating cellulase production in Neurospora crassa. Method: mRNA from vib-1 mutants were collected after a culture shift from sucrose to Avicel (crystaline cellulose) or carbon-free media. Expression profiles of vib-1 mutants were compared with published profiles of wild type created under the same conditions. Results: We found that many genes that specifically upregulated in wild type upon exposure to Avicel were expressed at low levels in ∆vib-1 and many other genes involved in metabolism and energy were expressed at high levels compared to wild type. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17918 GPL16164

9 Samples

Download data: FPKM_TRACKING

(Submitter supplied) In order to obtain genetically engineering strain of Penicillium oxalicum with high Raw Starch Digesting Glucoamylase production,we deleted PoxCxrC and overexpressed POX_f08097 in Penicillium oxalicum TE4-10 ,and we want to investigating the function of deletion of PoxCxrC and overexpression of POX_f08097 at transcriptional level.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32390

6 Samples

Download data: TXT

(Submitter supplied) The filamentous fungus Penicillium oxalicum can secret various enzymes for efficient saccharification of plant biomass materials. Expression of the constitutively active forms of transcriptional activators ClrB, XlnR and AraR could trigger the production of different sets of lignocellulolytic enzymes. Here, the transcriptomes of the three engineered strains were compared with that of wild type in the medium without carbon source.

Organism:

Penicillium oxalicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25605

12 Samples

Download data: TXT