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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB)

ABSTRACT: Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay. Two-condition experiment : A. niger mutant strains on SEB for 12 and 24 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to SEB as carbon source.

ORGANISM(S): Aspergillus niger

SUBMITTER: Wagner de Souza

PROVIDER: E-GEOD-37758 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Aspergillus niger mutants: induction by various carbon sources

Project description:This SuperSeries is composed of the following subset Series: GSE37758: Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB) GSE37760: Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA) Refer to individual Series

2012-05-06 | E-GEOD-37795 | biostudies-arrayexpress

Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA)

Project description:Transcriptional profiling of A. niger comparing different strains (WT, M-NM-^TXlnR, M-NM-^TaraR and M-NM-^TaraRM-NM-^TXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays. Two-condition experiment : A. niger mutant strains on XA for 2 and 8 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to xylose+arabinose (25 mM each) as carbon source.

2012-05-06 | E-GEOD-37760 | biostudies-arrayexpress

Aspergillus nidulans WT, M-NM-^TcrzA and M-NM-^TcrzA/scrA-: Control vs. calcium pulse

Project description:The main objective was to identifiy genes related to scrA- extragenic suppression of crzA. Thus, through transcriptional profiling, we characterised the transcriptional basis of calcium tolerance in our mutant strain, M-NM-^TcrzA/scrA-. To evaluate the effect of calcium on global A. nidulans gene expression, we performed competitive microarray hybridizations using RNA obtained from the wild-type, M-NM-^TcrzA and M-NM-^TcrzA/scrA- strains before and after short pulses (10 and 30 minutes) of 200 mM calcium chloride. The experiment was further validated by real-time PCR. Two-condition experiment : A. nidulans wild-type, M-NM-^TcrzA and M-NM-^TcrzA/scrA- strains with 200 mM CaCl2 for 10 and 30 min at 30M-BM-0C and 150 rpm in 25 mL YAG medium. Firstly, the strains were grown overnight at 30M-BM-0C and 150 rpm in YAG medium (preculture). Afterwards, the medium was switched by a new media (25 mL) plus calcium and incubated as described above. Control condition refers to the preculture in YAG medium without further incubation.

2012-05-22 | E-GEOD-38131 | biostudies-arrayexpress

Aspergillus nidulans : Control (Wt) vs. M-NM-^TcnaA or alcApkcAM-NM-^TcnaA

Project description:Transcriptional profiling of A. nidulans comparing the mutant strain alcApkcA M-NM-^TcnaA and M-NM-^TcnaA grown on alcA inducing conditions. The main objective was to identifiy genes related to M-NM-^TcnaA phenotype supression by pkcA overexpression. The experiment was further validated by real-time PCR. Two-condition experiment : A. nidulans strains grown during 24 and 48 h at 37oC in glycerol 2% threonine 100mM.

2013-07-04 | E-GEOD-48535 | biostudies-arrayexpress

Aspergillus nidulans: Control (Wt) vs. GPCRs mutants (M-NM-^TgprB and M-NM-^TgprD)

Project description:Transcriptional profiling of A. nidulans comparing the mutant strains M-NM-^TgprB and M-NM-^TgprD grown on 1% glucose (w/v) in a batch cultivation medium (BCM) at 37M-BM-0C for 24 and 48h. The main objective was to identifiy genes related to gprB and gprD gene function. The experiment was further validated by real-time PCR and enzymatic assay. Two-condition experiment : A. nidulans strains grown during 24 and 48 h at 37M-BM-0C in glucose 1% (w/v).

2012-11-28 | E-GEOD-42553 | biostudies-arrayexpress

Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB)

Project description:Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (ΔXlnR, ΔaraR and ΔaraRΔXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay.

2012-05-07 | GSE37758 | GEO

Aspergillus nidulans: Control (0 h starvation) vs. induction of starvation (12 h and 24 h) for WT, delta xprG and delta atmA

Project description:Transcriptional profiling of A. nidulans comparing starvation for 0 (reference), 12 and 24 h. The main objective was to identify genes specifically regulated during starvation by atmA and xprG. The results of the experiment were further validated by real-time PCR. Experimental procedure: Three A. nidulans strains were used in this study: WT, delta atmA and delta xprG. Strains were grown on minimal medium for 24 h (0 h starvation reference), then exposed to 12 and 24 h starvation. atmA: ATM, Ataxia-Telangiectasia mutated; Malavazi, I., Savoldi, M., Da Silva Ferreira, M. E., Soriani, F. M., Bonato, P. S., De Souza Goldman, M. H. and Goldman, G. H. (2007), Transcriptome analysis of the Aspergillus nidulans AtmA (ATM, Ataxia-Telangiectasia mutated) null mutant. Molecular Microbiology, 66: 74-99 (PMID 17880424). xprG: extracellular protease; Margaret E. Katz, Karen-Ann Gray, Brian F. Cheetham, (2006) The Aspergillus nidulans xprG (phoG) gene encodes a putative transcriptional activator involved in the response to nutrient limitation, Fungal Genetics and Biology, 43, 190-199 (PMID 16464624).

2012-12-07 | E-GEOD-42732 | biostudies-arrayexpress

Aspergillus nidulans strains TNO2a3 and M-bM-^HM-^FptpB (AN4896) grown on casaminoacids as sole carbon source transfer to glucose

Project description:Transcriptome of A. nidulans TNO2a3 and M-bM-^HM-^FptpB strains when grown on minimal media plus casaminoacids and transferred to minimal media plus glucose as a sole carbon source for 4 hours Three conditions minimal media plus casaminoacids during 24 hours (reference) and minimal media plus glucose for 4 hours. Three strains TNO2a3 and M-bM-^HM-^FptpB. Three biological repetitions of each timepoint of TNO2a3 / M-bM-^HM-^FptpB

2014-10-03 | E-GEOD-61980 | biostudies-arrayexpress

Aspergillus nidulans strains TNO2A3, M-bM-^HM-^FmsbA and M-bM-^HM-^FMHD grown in complete media (YUU) and on avicel as sole carbon source

Project description:Transcriptome of A. nidulans TNO2A3, M-bM-^HM-^FmsbA and M-bM-^HM-^FMHD strains when grown on complete media (YUU) and transferred to minimal media plus avicel as a sole carbon source for 24 hours Two conditions: complete media (reference) for 24h and minimal media plus avicel for 24 hours. Three strains TNO2A3, M-bM-^HM-^FmsbA and M-bM-^HM-^FMHD. Three biological repetitions of each point.

2015-01-01 | E-GEOD-60594 | biostudies-arrayexpress

Gene expression profiles of human breast cancer cell lines

Project description:Numerous epithelial-to-mesenchymal transition (EMT)-promoting transcription factors have been implicated in tumorigenesis or metastasis, as well as chemoresistance of cancer. However, the underlying mechanism mediating these processes is unclear. Here we report that Foxq1, a forkhead box-containing transcription factor and EMT-inducing gene, promotes stemness traits and chemoresistance in mammary epithelial cells. We identify Twist1, Zeb2, and PDGFRM-NM-1 and M-NM-2 as Foxq1 downstream targets using an expression profiling assay. Further studies reveal that PDGFRM-NM-1 and M-NM-2 can be directly regulated by Foxq1, or indirectly through Twist1. Knockdown of both PDGFRM-NM-1 and M-NM-2 shows more significant effects on reversing Foxq1-promoted oncogenesis in vitro and in vivo than knockdown by either PDGFRM-NM-1 or M-NM-2 alone. PDGFRM-NM-2, but not PDGFRM-NM-1, shows potent effects in reversing Foxq1-promoted stemness traits. Moreover, pharmacological inhibition or gene silencing of PDGFRs sensitize mammary epithelial cells to chemotherapeutic agents in vitro and in vivo. These findings collectively indicate PDGFRs as critical mediators underlying breast cancer tumorigenesis and chemoresistance driven by EMT promoting genes, which have potential clinical implications for cancer therapy. The purpose of these experiments is to investigate the downstream targets of several transcriptional factors including Foxq1 and IRX5. Another purpose is to compare the expression pattern between basal-like breast cancer cells including MDA-MB231, SUM159 and SUM1315.

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