Aspergillus niger growing on SEB 6h - Replicate 1
For RNA sequencing (RNA-Seq), T. reesei and A. niger spores were first cultivated in potato dextrose agar plate for 7-10 days at 29°C and 30°C, respectively, and harvested by adding 1 mL of sterile distilled water. The spore suspensions were inoculated to a final concentration of 1 × 10⁶ spores per 30 mL of BCM culture in 250 mL flasks. T. reesei and A. niger spores were grown on BCM with 1% fructose (w/v) as the carbon source at 29°C and 30°C, respectively, for 24 hours (h) (A. niger) or 48 h (T. reesei) on a rotary shaker with agitation of 200 rpm and then transferred to either 0.5% SEB (w/v) as the carbon source for 6, 12 and 24 h, or 1% fructose (w/v) for 24 h to RNA-Seq experiment. The RNA-Seq experiments were carried out in duplicates. Fructose was used as control condition in all experiments because it is an inert sugar which does not induce neither suppresses overall expression of lignocellulolytic enzymes (Amore et al., 2013). For the growth of T. reesei, the cultures were maintained in constant light, as this influences positively cellulase gene expression (Schmoll et al., 2005). Mycelia were harvested by filtration through Whatman grade 1 filters (GE Healthcare, Grandview Blvd. Waukesha, WI, USA), washed thoroughly with sterile water and immediately ground into powder in liquid nitrogen. Aliquots of 100 mg ground mycelia were harvested and kept at -80 °C until the RNA extraction.    Total RNA from aliquots was extracted using the RNeasy Plant Mini kit (Qiagen) according to manufacturer’s instructions. RNA concentration was determined on a Nanodrop 2100c (Thermo Fisher Scientific, Waltham, MA, USA) and the integrity was evaluated on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the Agilent RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA). Total RNA of two biological replicates per condition (SEB or fructose) from both fungi was used as input for the TruSeq RNA Sample Prep v2 kit (Illumina, San Diego, CA, USA) and the libraries were sequenced by the USC Epigenome Center (CA, USA) using the Illumina® HiSeq2000 platform, producing single-end reads of 50 bp.