Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Mycelia were ground under liquid nitrogen using a mortar and pestle, then the RNA was purified using the Plant/Fungi total RNA Purification Kit (Norgen Biotek, Canada) including the on-column DNase treatment step. Total RNA was measured using Qubit RNA BR assay kit (Life technologies, Q10210). 1 µg of Total RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Illumina stranded whole transcriptome sequencing libraries were prepared using NEBNext Ultra Directional RNA library prep kit for Illumina (NEB, E7420S). Library QC was performed using bioanalyser HS kit (Agilent biotechnologies, 5067-4626). Libraries were quantified using qPCR (Kapa Biosystems, KK4824), pooled at desired concentrations, denatured and loaded for sequencing according to manufacturer's instructions. Sequencing was done on Illumina NextSeq500 sequencing platform using 2 high output runs to generate 2 x 75 bp reads. Sufficient sequencing was done to obtain ~30 M reads from each monoculture replicate and ~ 100 M reads from each mixed culture replicate. Note: For consistency and to avoid bias, all 30 samples were pooled for running on a lane which resulted in a read output for each sample from each of the four lanes from each of the two runs with the exception of sample BP-23 which was only run once. This would generate 480 sequencing files ((read files (total 2) from each sample (total 30) from each lane (total 4) for each run (total 2)) = 2 x 30 x 4 x 2 = 480) except only 472 files were generated as sample BP-23 was only run in run 1.