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| Status |
Public on Apr 18, 2016 |
| Title |
Aspergillus nidulans grown in 0.7M of cholinium chloride media for fifteen days, biological rep. 3 |
| Sample type |
RNA |
| |
|
| Source name |
Aspergillus nidulans mycelia after growth in 0.7M of cholinium chloride media for fifteen days
|
| Organism |
Aspergillus nidulans |
| Characteristics |
culture conditions: Fifteen days in 0.7M of cholinium chloride media
|
| Treatment protocol |
Aspergillus nidulans (FGSC A4) cultures were incubated with 1.00E+5 conidia per mL (50 mL), in the dark, at 27 °C and with 70% humidity and under orbital agitation (90 rpm), for fifteen days. The media used was minimal media containing 0.1% w/v glucose (control), minimal media with 0.1% w/v glucose supplemented with cholinium chloride (0.7M) and minimal media with 0.1% w/v glucose supplemented with 1-ethyl-3-methylimidazolium chloride (0.7M). After fifteen days the mycelia and the culture media were recovered and preserved at -80 °C.
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| Growth protocol |
Fungal cultures with a density of Aspergillus nidulans (FGSC A4) conidia of 1.00E+5 per mL (50 mL, minimal media containing 0.1% w/v glucose) were incubated in the dark, at 27 °C and with 70% humidity, under orbital agitation (90 rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from fungal mycelia (grounded to powder using mortar and pestle in liquid nitrogen) using the RNeasy Plant Mini Kit (QIAGEN) and further purified following a standard ethanol precipitation.
|
| Label |
biotin
|
| Label protocol |
RNA was processed for use on Affymetrix custom dual species FungiANC arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.
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|
| Hybridization protocol |
A total of 200µl of the hybridisation mixture containing 10µg of fragmented cRNA was hybridised on arrays for 16 hours at 45 °C. Standard post hybridisation washes and double-stain protocols (FS450_0001) were used on an Affymetrix GeneChip Fluidics Station 450, in conjunction with the GeneChip Hybridisation Wash and Stain Kit (Affymetrix).
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| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.
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| Description |
Gene expression data A. nidulans grown in 0.7M of cholinium chloride media for fifteen days
|
| Data processing |
Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org) applying a probeset mask file considering only the A. nidulans probes on the array representing 9674 transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the 9 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model.
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| |
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| Submission date |
Feb 14, 2015 |
| Last update date |
Apr 18, 2016 |
| Contact name |
Cristina Silva Pereira |
| E-mail(s) |
spereira@itqb.unl.pt
|
| Organization name |
Instituto de Tecnologia Química e Biológica (ITQB)
|
| Lab |
Applied and Environmental Mycology Laboratory (AEM)
|
| Street address |
Rua da Quinta Grande nº6
|
| City |
Lisboa |
| ZIP/Postal code |
2780-156 Oeiras |
| Country |
Portugal |
| |
|
| Platform ID |
GPL18227 |
| Series (1) |
| GSE65946 |
Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans |
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