|
| Status |
Public on Apr 12, 2016 |
| Title |
Transgenic NA1363 Strain Replicate 6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
transgenic NA1363 strain (LacZ)
|
| Organism |
Aspergillus nidulans |
| Characteristics |
strain: NA1363 (pabaA1) harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in chromosome VIII. This construct, carried out in a derivative of the pBR322 vector, contained the E. coli lacZ sequence (encoding ß-galactosidase) fused to the A. nidulans trpC terminator and placed under the control of the strong and constitutive promoter of the A. nidulans gpdA gene, and the riboB gene as selection marker.
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) 2 of 2. Individual culture 2 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. |
|
