Platform

Substrate

Sample condition

RNA-seq data analysis

Reference

Roche NimbleGen arrays

microcrystalline cellulose

Three biological replicates; total RNA was extracted from frozen fungi pellets after 5 days incubation at 37˚C

NimbleScan v2.4 and ArrayStar v2.1 software was used to quantify and visualize data. Quantile normalization and robust multi-array averaging were applied to the entire data set. Expression levels are based on log2 values.

[33]

Roche NimbleGen arrays

ball-milled aspen

Three biological replicates; total RNA was extracted from frozen fungi pellets after 5 days incubation at 37˚C

DNASTAR ArrayStar v2.1 software was used to quantify and visualize data. Quantile normalization and robust multiarray averaging were applied to the entire data set. Expression levels are based on log2 values. T-test with a false discovery rate threshold at P < 0.001 was used to determine significant differences in expression.

[34]

Illumina HiSeq 2000

Spruce wood

Three biological replicates; total RNA was extracted from samples at 40 h and 96 h incubation at 38˚C

DNAStar Inc. modules SeqNGen and Qseq were used for mapping reads and statistical analysis. The current Joint Genome Institute (JGI) annotation (v2.2), served as the queried database RNA-seq-based transcript results are presented as RPKM values

[35]

Illumina HiSeq 4000

Maple wood and miscanthus

Three biological replicates; RNA was extracted from mycelium after 5 weeks cultivation at room temperature.

ArrayStar program of DNASTAR software was used to process raw data sequences, and annotation was done by using the P. chrysosporium RP-78 v2.2 from the Joint Genome Institute

(JGI). RNA-seq transcript-based results were reported as RPKM values

[36]

Illumina HiSeq 4000

Helianthus argophyllus (silverleaf sunflower) stem

Three biological replicates; RNA was extracted from samples after 6 weeks incubation at room temperature

ArrayStar program of DNASTAR software was used to process the raw data sequences, the annotation was done using P. chrysosporium RP-78 v2.2 and Gene Ontology (GO) file (Phchr 2 _GeneCatalog_proteins _ 20131210

_GO.tab.gz) from the Joint Genome Institute (JGI).

NCBI nucleotide BLAST was further used to annotate transcripts of interests. The data were represented as RPKM values.

[37]