cell type: Mycelia strain: TL01 cultured medium: rice-peanut cake based industrial fermentation medium
Treatment protocol
The mycelia was collected from the fermentation medium by centrifugation at 12,000 rpm for 5 min, resuspended in 1 mL TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US), and broken in a precellys homogenizer (6,500 rpm, 1×30 s; Peqlab) with glass beads (150–212 μm, Sigma). Cell debris was removed by centrifugation at 12,000 rpm for 5 min, and the extracted supernatants were stored at -80°C.
Growth protocol
Strain 5008 and TL01 were pre-cultured at 30°C for 48 h in 50 ml TSB liquid medium plus 1 % yeast extract in 250 ml shaking flasks with reciprocal shaking (220 rpm). 0.5 ml of each culture was inoculated 50 ml laboratory fermentation medium Yeast extract-Malt extract-Glucose (YMG) and 50 ml rice-peanut cake based industrial (IND) fermentation medium in three 250 ml shaking flasks. The batch cultures were incubated at 37°C for 48 h (220 rpm).
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label
Cy3
Label protocol
Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
Hybridization protocol
Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.
Scan protocol
Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)
Description
Gene expression at TL01 cultured in IND medium
Data processing
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
