|
| Status |
Public on Apr 12, 2016 |
| Title |
Control CV125 Strain Replicate 8 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
control CV125 strain (WT)
|
| Organism |
Aspergillus nidulans |
| Characteristics |
strain: CV125 (pabaA1)
tissue: mycelium
|
| Treatment protocol |
None
|
| Growth protocol |
Mycelia were grown at 30°C for 15 h in 400 mL minimal medium with shaking at 150 rpm, in the presence of fructose (0.1%) as the carbon source and urea (5 mM) as the nitrogen source. Media composition, supplements and basic growth conditions were as described by Cove DJ (Biochim Biophys Acta. 1966 Jan 11;113(1):51-6. PMID: 5940632 1966). For each strain, 4 cultures were carried out in each one of two independent experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as previously described (Total RNA was isolated with guanidine as described (Robellet X et al. 2010 Curr Genet. 2010 56(4):341-8. doi: 10.1007/s00294-010-0303-5. Epub 2010 May 22). An additional purification step was performed using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA were labelled using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent Technologies), using Cy5-CTP for the reference RNA pool made of a mix of all samples, and Cy3-CTP for individual samples.
|
| |
|
| Channel 2 |
| Source name |
pooled WT and TG strains
|
| Organism |
Aspergillus nidulans |
| Characteristics |
strain: mix of 4 strains CV125 (pabaA1) and 3 transgenic (pabaA1) strains harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in different chromosomes (NA1363, in chromosome VIII; NA1360, in chromosome V; NA1359, in chromosome II).
tissue: mycelium
|
| Treatment protocol |
None
|
| Growth protocol |
Mycelia were grown at 30°C for 15 h in 400 mL minimal medium with shaking at 150 rpm, in the presence of fructose (0.1%) as the carbon source and urea (5 mM) as the nitrogen source. Media composition, supplements and basic growth conditions were as described by Cove DJ (Biochim Biophys Acta. 1966 Jan 11;113(1):51-6. PMID: 5940632 1966). For each strain, 4 cultures were carried out in each one of two independent experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as previously described (Total RNA was isolated with guanidine as described (Robellet X et al. 2010 Curr Genet. 2010 56(4):341-8. doi: 10.1007/s00294-010-0303-5. Epub 2010 May 22). An additional purification step was performed using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
200 ng of total RNA were labelled using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent Technologies), using Cy5-CTP for the reference RNA pool made of a mix of all samples, and Cy3-CTP for individual samples.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After washing, slides were scanned using the Agilent Microarray Scanner (G2565CA) at 5-µm resolution.
|
| Scan protocol |
After washing, slides were scanned using the Microarray Scanner (G2565CA) from Agilent at 5-µm resolution and at high and low photomultiplier voltages. Images were quantified using Agilent Feature Extraction 10.7.3.1. software with default protocols and settings.
|
| Description |
Biological replicate (culture batch) 1 of 2. Individual culture 4 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.
|
| Data processing |
Data were computed using Genespring GX software version 12.6 (Agilent Technologies). Fluorescence signals were background-subtracted and a filtering procedure excluded data points considered unreliable as they corresponded to probe sets associated with low signal intensities or bad quality features. A within-array loess normalization was performed, followed by an inter-array scaling normalization.
|
| |
|
| Submission date |
Jan 15, 2016 |
| Last update date |
Apr 12, 2016 |
| Contact name |
Claudine DELOMENIE |
| E-mail(s) |
claudine.delomenie@u-psud.fr
|
| Phone |
33 1 46 83 57 85
|
| Organization name |
University Paris Sud 11
|
| Department |
Transcriptomique
|
| Lab |
Plate-forme Trans-Prot
|
| Street address |
5, rue Jean-Baptiste Clément
|
| City |
CHATENAY-MALABRY |
| ZIP/Postal code |
92296 |
| Country |
France |
| |
|
| Platform ID |
GPL21331 |
| Series (1) |
| GSE76918 |
Comparison of two A. nidulans strains: control CV125 and transgenic NA1363 harboring E. coli LacZ transgene. |
|
