|
| Status |
Public on Jul 16, 2013 |
| Title |
TNO_CMvsAvicel_8h_B |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TNO, CM, 24h
|
| Organism |
Aspergillus nidulans |
| Characteristics |
strain: TNO2a3
treatment: complete media
time point: 24h
|
| Growth protocol |
All A. nidulans strains were grown in CM for 24h, washed twice with dH2O and then transferred to MM plus avicel as a sole carbon source for 8 or 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy® Plant Mini Kit (Qiagen) following manufacturer's instructions, followed by DNase treatment and purification using RNeasy® Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for CM samples) or Cyanine-5 (for avicel samples) for 2 hours at 40 oC.
|
| |
|
| Channel 2 |
| Source name |
TNO, Avicel, 8h
|
| Organism |
Aspergillus nidulans |
| Characteristics |
strain: TNO2a3
treatment: avicel
time point: 8h
|
| Growth protocol |
All A. nidulans strains were grown in CM for 24h, washed twice with dH2O and then transferred to MM plus avicel as a sole carbon source for 8 or 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy® Plant Mini Kit (Qiagen) following manufacturer's instructions, followed by DNase treatment and purification using RNeasy® Mini Kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for CM samples) or Cyanine-5 (for avicel samples) for 2 hours at 40 oC.
|
| |
|
| |
| Hybridization protocol |
For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent's instruction.
|
| Scan protocol |
Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).
|
| Description |
Biological rep 2 of 3.
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After, data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).
|
| |
|
| Submission date |
Jun 10, 2013 |
| Last update date |
Jul 16, 2013 |
| Contact name |
Neil Brown |
| Organization name |
USP
|
| Street address |
Av. do Cafe
|
| City |
Ribeirao Preto |
| ZIP/Postal code |
14040903 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL15870 |
| Series (1) |
| GSE47810 |
Aspergillus nidulans strains TNO2a3, ∆snfA and ∆schA grown on avicel as sole carbon source |
|
