strain: QM9414 phenotype: low cellulase producing mutant time: 3 h
Treatment protocol
Sporulating mycelia were scraped off the cellophane, washed with distilled cold water, frozen and ground under liquid nitrogen.
Growth protocol
T. reesei QM9414 (ATCC 26921), an early cellulase producing mutant was used throughout this work and kept on potato dextrose agar. To induce conidiation in T. reesei, the fungus was grown on malt extract (MEX) agar plates (11 cm diameter) on a layer of cellophane to facilitate removal of mycelia. The formation of conidia was followed microscopically and by measuring a marker enzyme, the D-mannitol dehydrogenase LXR1. Samples of at least two biological replicas were taken at appropriate time points (see results).
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.
Description
from T. reesei QM 9414
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.).
