GEO DataSets

(Submitter supplied) 1.) Background: Gene expression profiling is a highly sensitive technique which is used for profiling of tumor samples for medical prognosis. RNA quality and degradation influences the analysis results of gene expression profiles. The impact of this influence on the profiles and its medical impact is not fully understood. As patient samples are very valuable for clinical studies, it is necessary to establish criteria for the RNA quality to use these samples in later analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

12 Samples

Download data: TXT

(Submitter supplied) The COP9 signalosome complex (CSN) is a crucial regulator of ubiquitin ligases. Defects in CSN result in embryonic impairment and death in higher eukaryotes, whereas the filamentous fungus Aspergillus nidulans survives without CSN, but is unable to complete sexual development. We investigated overall impact of CSN activity on A. nidulans cells by combined transcriptome, proteome and metabolome analysis. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL10563

32 Samples

Download data: CSV

(Submitter supplied) The COP9 signalosome (CSN) is a highly conserved eukaryotic protein complex which regulates the Cullin-RING family of ubiquitin ligases and carries out a deneddylase activity that resides in subunit 5 (CSN5). The budding yeast CSN is biochemically active and deletion mutants of each of its subunits exhibit deficiency in deneddylation of cullins, although the biological context of this activity is still unknown in this organism. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL14755

2 Samples

Download data: GPR

(Submitter supplied) Glutathione (GSH) is an abundant and widely distributed antioxidant in fungi. Hence, understanding cellular GSH metabolism is of vital importance to deciphering redox regulation in these microorganisms. In this study, we generated dugB (AN1879), dugC (AN1092), and dugB dugC double deletion mutants which display disruption of the GSH degradation pathway in Aspergillus nidulans. Deletion of dugB, dugC or both resulted in a moderate increase in GSH content under growing conditions and substantially slowed down the depletion of GSH pools under carbon starvation. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28598

12 Samples

Download data: XLSX

(Submitter supplied) The COP9 signalosome (CSN), an eight-subunit protein complex, is conserved in all higher eukaryotes. CSN intersects the ubiquitin-proteasome pathway, modulating signaling pathways controlling various aspects of development. We are using Drosophila as a model system to elucidate the function of this important complex. Transcriptome data was generated for four csn mutants, sampled at three developmental time points. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL4285

51 Samples

Download data: GPR

(Submitter supplied) CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL5620

13 Samples

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(Submitter supplied) CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5620

5 Samples

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(Submitter supplied) CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5620

8 Samples

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(Submitter supplied) This study aims to determine the downstream impact of cell wall perturbation on the filamentous fungus, Aspergillus nidulans.Fungi were treated with micafungin during mid-exponential growth phase and RNA-sequencing was performed at 0, 5, 10, 15, 20, 25, 30, 40, 50, 60, 75, 90, and 120 minutes of exposure in 3 biological replicates.

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27160

38 Samples

Download data: XLSX

(Submitter supplied) A transcriptomic assessment of a kinase deletion mutant (ΔmpkA) and a control strain revealed many cellular activities this kinase is impacting. Studies were conducted in the model filamentous fungi, Aspergillus nidulans¸ under rich growth conditions. MpkA is a known kinase involved in the cell wall integrity signaling pathway. This pathway is activated upon cell wall stress and regulates production of cell wall related genes. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23050

4 Samples

Download data: TXT

(Submitter supplied) The study aims essentially in the analysis of the transcriptomic and metabolomic profiles induced by the presence of the tested ionic liquids in the metabolism of Aspergillus nidulans. Focusing specially on the secondary metabolism, which genes are clustered.

Organism:

Aspergillus nidulans FGSC A4; Aspergillus nidulans; Neurospora crassa OR74A

Type:

Expression profiling by array

Platform:

GPL18227

9 Samples

Download data: CEL

(Submitter supplied) We examined the transcriptional changes observable under oxidative stress caused by menadione in Emericella nidulans. Keywords: time-course

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL1752

2 Samples

Download data: GPR

(Submitter supplied) Late exponential growth phase (18 h) Emericella nidulans mycelia were transferred to minimal media also supplemented with 1.8 mM diamide, 75 mM H2O2 or 0.8 mM menadione (sodium bisulfite addition compound) and transcriptome profiles were recorded at 0.25, 0.5, 1, 3, 6 and 9 h incubation times. Double printed EST-based (2x4352 spots) DNA chips were used to monitor changes in cDNA populations prepared from mRNA pools isolated from oxidative stress exposed and untreated control cultures. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL1756

32 Samples

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(Submitter supplied) Late exponential growth phase (18 h) Emericella nidulans mycelia were transferred to minimal media also supplemented with 1.8 mM diamide, 75 mM H2O2 or 0.8 mM menadione (sodium bisulfite addition compound) and transcriptome profiles were recorded at 0.25, 0.5, 1, 3, 6 and 9 h incubation times. Double printed EST-based (3533 unique sequences) DNA chips were used to monitor changes in cDNA populations prepared from mRNA pools isolated from oxidative stress exposed and untreated control cultures. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Dataset:

GDS1764

Platform:

GPL1752

16 Samples

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Analysis of mycelia at various timepoints up to 9 hours after exposure to diamide, H2O2, or menadione. Specific cell functions are involved in the resistance to each oxidative stress-inducing agent. Results identify transcriptional responses unique to diamide, H2O2, and menadione.

Organism:

Aspergillus nidulans

Type:

Expression profiling by array, log2 ratio, 3 agent, 6 time sets

Platform:

GPL1752

Series:

GSE2085

16 Samples

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(Submitter supplied) Transcriptional profiling of Aspergillus nidulans comparing control (growing on glucose) and carbon starving cultures.

Organism:

Aspergillus nidulans FGSC A4; Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL16338

1 Sample

Download data: TXT

(Submitter supplied) This study is the continuation of our previous study (Emri et al. BMC Genomics. 2015;16:478. doi: 10.1186/s12864-015-1705-z.). Here, we tested further three stress conditions using the same DNA chips, strains and culturing conditions as in our previous work. We combined the old and the new data sets to study the existence of environmental stress response in A. nidulans.

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL19388

8 Samples

Download data: TXT

(Submitter supplied) For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

28 Samples

Download data: TXT

(Submitter supplied) Background: The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma cells in surgically excised carcinoma tissues might obscure the tumor cell-specific gene expression profiles of these samples. To circumvent this complication, laser microdissection can be performed to separate tumor epithelium from the surrounding stroma and healthy tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2130

44 Samples

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(Submitter supplied) We created RNA with different degree of degradation and investigated if the RNA quality influenced gene expression We used oligo-cDNA-microarrays to compare gene expressions Keywords: RNA quality, breast cancer, gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5345

24 Samples

Download data: GPR