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] |