|
| Status |
Public on Oct 03, 2016 |
| Title |
SOPH_DD_2 |
| Sample type |
RNA |
| |
|
| Source name |
growth on sophorose in constant darkness
|
| Organism |
Trichoderma reesei |
| Characteristics |
genotype: wild-type
|
| Treatment protocol |
Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.
|
| Growth protocol |
Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% of the indicated carbon source or 1.5 mM sophorose in constant light (LL) or constant darkness (DD) for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
one of two biological replicates
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 12, 2016 |
| Last update date |
Oct 03, 2016 |
| Contact name |
Monika Schmoll |
| E-mail(s) |
monika.schmoll@univie.ac.at
|
| Organization name |
University of Vienna
|
| Department |
Centre of Microbiology and Environmental Systems Science
|
| Lab |
Division of Terrestrial Ecosystem Research
|
| Street address |
Djerassiplatz 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL10642 |
| Series (1) |
| GSE81365 |
Transcriptome analysis of T. reesei upon growth on different carbon sources in light and darkness |
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