Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.
Growth protocol
Trichoderma reesei strain QM9414 (ATCC 26921) was grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1 % microcrystalline cellulose as carbon source 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 Random Hexamer 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
QM9414_DD_replicate 1
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.).
