Transcriptome changes in Emericella nidulans due to oxidative stress - normalized experimental data (flip-flop)
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ABSTRACT:
ORGANISM(S): Aspergillus nidulans
PROVIDER: GSE4713 | GEO | 2010/03/01
SECONDARY ACCESSION(S): PRJNA95599
REPOSITORIES: GEO
Similar Datasets
Project description: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. Gene expression ratios were estimated with Genisphere (Hatfield, PA, USA) 3DNA Submicro EX Expression Array Detection Kit. Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software. Gene expression ratios were subjected to LOESS-type block-by-block normalization using SAS for Windows, version 8. (SAS Institute Inc., Cary, NC, USA.) software. Global gene expression profiles were correlated to physiological changes quantified by intracellular reactive oxygen species levels and redox balances. Primary unprocessed experimental data are summarized Series GSE2100. Keywords: time-course
2006-01-05 | GSE2085 | GEO
Project description: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. Gene expression ratios were estimated with Genisphere (Hatfield, PA, USA) 3DNA Submicro EX Expression Array Detection Kit. Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software. Note, processed data after LOESS-type normalization are presented on Series GSE2085 and all the signs were also reversed during data processing to reach proper log2(treated/control) channel intensity ratios. Keywords: time-course
2006-01-05 | GSE2100 | GEO
Project description:Genome wide transcriptional changes induced by various types of oxidative stresses as well as salt stress were studied in a DatfA mutant and the appropriate control A. nidulans strains. Although a significant number of stereotypically regulated genes was identified (Core Oxidative Stress Response or COSR genes) when the global transcriptional effects of five different oxidative stress conditions were compared the number of co-regulated genes decreased to 13 when NaCl stress was included into the analyses. The appearance of only a few co-regulated genes and the great number of genes regulated merely by one certain type of stress do not support the existence of a S. cerevisiae-type Environmental Stress Response in A. nidulans. Deletion of atfA, a true functional ortholog of fission yeastâs âall-purposeâ stress response transcription factor, increased the oxidative stress sensitivity of A. nidulans and affected the transcription of several genes under both unstressed and stressed conditions. The number of genes under AtfA control was quite stress-type dependent; e.g. deletion of atfA altered the transcription of a wide spectrum of genes under menadione sodium bisulfite stress but had only a minor effect on the transcriptome profiles when A. nidulans cultures were exposed to H2O2, tBOOH, NaCl and, especially, to diamide stress. These observations suggest that the function of AtfA in the regulation of various stress responses is much smaller than we thought before or other transcription factors can take over a number of AtfAâs functions when the atfA gene is deleted. It is noteworthy that both oxidative and salt stress induced the transcription of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of further clusters. Surprisingly, certain clusters were down-regulated by the stress conditions tested and the majority of them were not stress-responsive at all. Therefore, stress dependent regulation seems to be a frequent but far not a general feature of the regulation of secondary metabolism in A. nidulans. 14 samples, 7 with the control strain and 7 with an DatfA strain (each series contains samples from untreated as well as menadione, low concentration hidrogen-peroxide, high concentration hidrogen-peroxide, tert-butylhydroperoxide, diamide and NaCl treated cultures)
2015-12-31 | E-GEOD-63019 | biostudies-arrayexpress
Project description:Genome wide transcriptional changes induced by various types of oxidative stresses as well as salt stress were studied in a DatfA mutant and the appropriate control A. nidulans strains. Although a significant number of stereotypically regulated genes was identified (Core Oxidative Stress Response or COSR genes) when the global transcriptional effects of five different oxidative stress conditions were compared the number of co-regulated genes decreased to 13 when NaCl stress was included into the analyses. The appearance of only a few co-regulated genes and the great number of genes regulated merely by one certain type of stress do not support the existence of a S. cerevisiae-type Environmental Stress Response in A. nidulans. Deletion of atfA, a true functional ortholog of fission yeast’s “all-purpose” stress response transcription factor, increased the oxidative stress sensitivity of A. nidulans and affected the transcription of several genes under both unstressed and stressed conditions. The number of genes under AtfA control was quite stress-type dependent; e.g. deletion of atfA altered the transcription of a wide spectrum of genes under menadione sodium bisulfite stress but had only a minor effect on the transcriptome profiles when A. nidulans cultures were exposed to H2O2, tBOOH, NaCl and, especially, to diamide stress. These observations suggest that the function of AtfA in the regulation of various stress responses is much smaller than we thought before or other transcription factors can take over a number of AtfA’s functions when the atfA gene is deleted. It is noteworthy that both oxidative and salt stress induced the transcription of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of further clusters. Surprisingly, certain clusters were down-regulated by the stress conditions tested and the majority of them were not stress-responsive at all. Therefore, stress dependent regulation seems to be a frequent but far not a general feature of the regulation of secondary metabolism in A. nidulans.
2015-12-31 | GSE63019 | GEO
Project description:Oxidative stress caused by Menadione or Hydrogen peroxide in synchronized Saccharomyces cerevisiae cultures. Alpha factor synchronized cultures (0.2-0.4 OD), treated at the beginning of S phase (25 min after release from G1 arrest) with either 2 mM Menadione (MD) or 0.24 mM Hydrogen peroxide (HP), show cell cycle effects. Cells treated with MD arrested at G1. Cells treated with HP delayed at S and then, after removal of HP at 135 minutes , continued the cell cycle, only to arrest at G2/M. Growth was carried out in 30C with shaking (295 rpm). Two time course experiments were performed with each oxidative stress agent, designated as H2O2 and H2O2_II, MD and MD_II. Keywords = oxidative stress Keywords = menadione Keywords = hydrogen peroxide Keywords = time course Keywords = cell cycle Keywords = yeast Keywords: other
2005-02-04 | GSE2239 | GEO
Project description:Oxidative stress caused by Menadione or Hydrogen peroxide in synchronized Saccharomyces cerevisiae cultures. Alpha factor synchronized cultures (0.2-0.4 OD), treated at the beginning of S phase (25 min after release from G1 arrest) with either 2 mM Menadione (MD) or 0.24 mM Hydrogen peroxide (HP), show cell cycle effects. Cells treated with MD arrested at G1. Cells treated with HP delayed at S and then, after removal of HP at 135 minutes , continued the cell cycle, only to arrest at G2/M. Growth was carried out in 30C with shaking (295 rpm). Two time course experiments were performed with each oxidative stress agent, designated as H2O2 and H2O2_II, MD and MD_II. Keywords = oxidative stress Keywords = menadione Keywords = hydrogen peroxide Keywords = time course Keywords = cell cycle Keywords = yeast
2005-02-04 | E-GEOD-2239 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA). A twelve array study using total RNA recovered from six separate cultures of Aspergillus nidulans wild-type RDIT9.32 (veA) and six separate cultures of Aspergillus nidulans overexpressing rsmA (restorer of secondary metabolism A), using custom-designed, four-plex arrays. The experiment was divided into two runs. In the first run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans carrying a plasmid overexpressing rsmA under the control of the gpdA promoter were assayed. In the second run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans overexpressing rsmA at the native locus under the control of the gpdA promoter were assayed.
2012-01-17 | E-GEOD-34220 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans AN1599 (PbcR) overexpression mutant, compared to the FGSC A4 wild-type strain. Overexpression of the Zn(II)2Cys6 –type transcription factor, AN1599.4 (PbcR, pimaradiene biosynthetic cluster regulator), activates a secondary metabolite gene cluster in Aspergillus nidulans. Activation of the pathway in Aspergillus nidulans lead to a production of ent-pimara-8(14),15-diene.
2012-04-16 | GSE32954 | GEO
Project description:Experimental evolution was conducted using Drosophila melanogaster populations that developed as larvae on breeding substrate that was infested with Aspergillus nidulans wild type, A. nidulans toxin-impaired mutant strain delta-laeA, the mycotoxin sterigmatocystin, or on fungi and toxin free substrate. Overall population were reared under these conditions for 11 generations, where after each confrontation generation one relaxation generation (fungi and toxin free breeding substrate) was conducted. Nine generations after the last selection treatment, first instar larvae were confronted with 3 days old A. nidulans wild type colonies or control conditions. 24 hours after confrontation start larvae were collected. For each biological replicate 52 larvae were collected from 4 independent confrontation units, balanced design. Three populations per selection regime were conducted, resulting in: 2 conditions x 4 selection regimes x 3 biological replicates (equal to fly population) = 24 samples. Selection regimes: sCO= control; sWT= A. nidulans wild type; sLA= A. nidulans mutant strain; sST= Sterigmatocystin. confrontation condition: cCO= control; cWT= A. nidulans wild type.
2020-05-09 | E-MTAB-9011 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. nidulans comparing Xylose and Fructose grown on Wild type strain. The main objective was to identifiy genes related to Xylose transport. The experiment was further validated by real-time PCR. Three-condition experiment : A. nidulans strains grown during 16 h on fructose and transfered to xylose for 6, 12 and 24h.
2013-08-31 | E-GEOD-50485 | biostudies-arrayexpress