The cells were harvested at 4 h by centrifugation at 10,000 rpm, 4 oC for 10 min, then quenched by liquid nitrogen and stored at -80 oC freezer for RNA extraction.
Growth protocol
G. oxydans was cultured in a 3 L bioreactor (Baoxing Biotech Co., Shanghai, China) containing one liter seed medium (80 g of sorbitol, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) at 30 ºC, pH 5.5, 2.5 vvm and 500 rpm to OD₆₀₀ reached 5.0. Then the seed broth was inoculated at 10% (v/v) ratio into 250 mL flask containing 45 mL synthetic fermentation medium (80 g of glucose, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) with the addition of 1.2 g/L furfural, 1.5 g/L of HMF, 0.8 g/L of HBA, 0.9 g/L of syringaldehyde or 0.8 g/L of vanillin, respectively at 30 ºC, 220 rpm.
Extracted molecule
total RNA
Extraction protocol
RNA was prepared using the Trizol (Invitrogen, Gaithersburg, MD, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label
Cy3
Label protocol
Cyanine-3 (Cy3) (GE Healthcare Cat. No. PA53021) labeled cRNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.
Hybridization protocol
According to the Agilent miRNA Microarray Protocol (Agilent Technologies).
Scan protocol
After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner (G2565CA) with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).
Description
258001210002_1_1 Gene expression with vanillin treatment 151581A&150948A_V3
Data processing
Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software V13 (Agilent) was used to calculate the difference of gene expression and statistical significance p value The normalized value of 75 percentile was calculated (log2). Note: Normalization is done using the Percentile75 method (the ratio is obtained by dividing the 75 bits value of the data expressed by each chip itself), and then the value generated after the logarithm of the log2 is taken.
