GEO DataSets

(Submitter supplied) Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL14949

23 Samples

Download data: GPR, TXT

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

Organism:

Neurospora crassa

Type:

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

Platform:

GPL16164

33 Samples

Download data: TXT

(Submitter supplied) abstract: The plant cell wall is composed of many complex polymers, and its deconstruction requires an equally complex orchestration of a wide array of enzymes. In Neurospora crassa, clr-1, clr-2 and xlr-1 have been identified as the key transcription factors involved in cell wall breakdown. In order to define their regulons, we performed ChIPseq upon these three transcription factors. CLR-1, CLR-2 and XLR-1 each bind to the most highly and differentially expressed gene populations, which include the cellulases for the CLRs and the hemicellulases for XLR-1. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16164

22 Samples

Download data: XLSX

(Submitter supplied) abstract: The plant cell wall is composed of many complex polymers, and its deconstruction requires an equally complex orchestration of a wide array of enzymes. In Neurospora crassa, clr-1, clr-2 and xlr-1 have been identified as the key transcription factors involved in cell wall breakdown. In order to define their regulons, we performed ChIPseq upon these three transcription factors. CLR-1, CLR-2 and XLR-1 each bind to the most highly and differentially expressed gene populations, which include the cellulases for the CLRs and the hemicellulases for XLR-1. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

11 Samples

Download data: 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:

Neurospora crassa OR74A; Aspergillus nidulans FGSC A4

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL16600 GPL15147

22 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in response to different light conditions of the T. reesei QM9414 deletion strains delta-blr1, delta-blr2 and delta env1 cultivated on 1% microcrystalline cellulose. Perception and proper interpretation of environmental signals is crucial for survival in any natural habitat. Although the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) is predominantly known for its capability of efficient plant cell wall degradation, recent studies show that it has not lost its evolutionary heritage. more...

Organism:

Trichoderma reesei

Type:

Expression profiling by array

Platform:

GPL10642

16 Samples

Download data: CALLS, PAIR

(Submitter supplied) Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enyzmes and the light response. The filamentous fungus, Neurospora crassa, has been used as a model organism to study light and circadian rhythm biology. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

20 Samples

Download data: GPR

(Submitter supplied) Sterol Regulatory Element Binding Proteins (SREBPs) are conserved from yeast to mammalian cells and function in regulating sterol homeostasis. In fungi, the SREBP pathway has been implicated in the adaptation to hypoxia and in virulence. In Neurospora crassa and Trichoderma reesei, the SREBP pathway also negatively regulates protein secretion under lignocellulolytic conditions. Here we utilized global transcriptional profiling combined with genetic and physiological analyses to address the regulatory link between the SREBP pathway and protein secretion in N. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23150

12 Samples

Download data: FPKM_TRACKING

(Submitter supplied) The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed by growth profiling, enzymatic activities, and transcriptomics on cellulose. more...

Organism:

Trichoderma harzianum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34038

18 Samples

Download data: TXT

(Submitter supplied) Filamentous fungi are powerful producers of hydrolytic enzymes for the deconstruction of plant cell wall polysaccharides. However, the central question of how these sugars are perceived in the context of the complex cell wall matrix remains largely elusive. To address this question in a systematic fashion we performed an extensive comparative systems analysis of how the model filamentous fungus Neurospora crassa responds to the three main cell wall polysaccharides: pectin, hemicellulose and cellulose. more...

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15146 GPL15147

15 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to investigate the role of the transcription factor Xyr1 in the regulation of cellulolytic and xylanolytic genes of the filamantous fungus Myceliophthora thermophila

Organism:

Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27455

20 Samples

Download data: XLS

(Submitter supplied) To study the consequences of transcription factor pp-1 deletion during vegetative cell fusion, we sequenced mRNA of WT and Δpp-1 conidia during a period of intense germling fusion activity .

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17654

2 Samples

Download data: TXT

(Submitter supplied) To study the consequences of transcription factor pp-1 deletion during vegetative cell fusion, we performed whole genome microarrays of WT and Δpp-1 conidia during their initial growth period (3h - 8h).

Organism:

Neurospora crassa; Neurospora crassa OR74A

Type:

Expression profiling by array

Platform:

GPL13956

35 Samples

Download data: GPR, TXT

(Submitter supplied) To study the consequences of MAK-2 activity modulation during vegetative cell fusion, we took advantage of a previously constructed allele of MAK-2 (MAK-2Q100G) to specifically perturb kinase signaling during germling vegetative cell fusion (inhibition of MAK-2Q100G activity by addition of the ATP analog 1NM-PP1 results in a phenotype indistinguishable from mak-2 deletion strains). Whole genome microarrays of mak-2Q100G cells following 20 min 1NM-PP1 treatment were performed.

Organism:

Neurospora crassa; Neurospora crassa OR74A

Type:

Expression profiling by array

Platform:

GPL13956

7 Samples

Download data: GPR

(Submitter supplied) Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30082

12 Samples

Download data: TXT, XLSX