strain: QM9414 tissue: mycelia medium: growth on glycerol for 24 hrs
Treatment protocol
Mycelia from both stages were freeze-dried and ground in liquid nitrogen using a mortar and pestle. For each of the two experimental conditions, five independent replicates of mycelium were mixed.
Growth protocol
Trichoderma reesei strain QM9414 (ATCC 26921) was grown in duplicate grown in 1 l Erlenmeyerflasks flasks on a rotary shaker (250 rpm) at 30 C in the medium described by Seiboth et al. (2004) [Mol Microbiol 51:1015-25] with lactose, glucose and glycerol (each two flasks) as a carbon source at a final concentration of 10 g l-1.
Extracted molecule
total RNA
Extraction protocol
Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.
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.
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.).
