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Table 1 Summary of datasets that were analyzed for overall transcriptome patterns

From: Fungal gene expression levels do not display a common mode of distribution

Sample Condition No. of peaks Main peaks1
Taphrinomycotina    
S. pombe run30_s7 YE medium, exponential growth 2 1
S. pombe run30_s8 YE medium, exponential growth 2 1
S. pombe run33_s1 meiosis, 0 h 2 2
S. pombe run33_s2 meiosis, 0 h 2 2
S. pombe run33_s3 meiosis, 1 + 2 h 2 2
S. pombe run33_s4 meiosis, 1 + 2 h 2 2
S. pombe run33_s5 meiosis, 3 + 4 h 2 2
S. pombe run33_s6 meiosis, 3 + 4 h 2 2
S. pombe run33_s7 meiosis, 5 + 6 h 2 2
S. pombe run34_s1 meiosis, 5 + 6 h 2 2
S. pombe run34_s2 meiosis, 7 + 8 h 2 2
S. pombe run34_s3 meiosis, 7 + 8 h 2 2
Saccharomycotina    
S. cerevisiae SRR453566 respiro-fermentative (batch) 3 1
S. cerevisiae SRR453567 respiro-fermentative (batch) 3 1
S. cerevisiae SRR453568 respiro-fermentative (batch) 3 1
S. cerevisiae SRR453569 fully respiratory (chemostat) 3 1
S. cerevisiae SRR453570 fully respiratory (chemostat) 3 2
S. cerevisiae SRR453571 fully respiratory (chemostat) 3 1
Pezizomycetes    
P. confluens GSM1020388/89 light grown, sexual mycelium 3 2
P. confluens GSM1020390/91 dark grown, vegetative mycelium 3 2
P. confluens GSM1020392/93 vegetative mycelium mix 3 2
T. melanosporum ERR019644 free-living mycelium 1 1
T. melanosporum ERR019645 fruiting bodies 3 1
T. melanosporum ERR019646 ectomycorrhizal root tips 3 1
Sordariomycetes    
N. crassa SRR400635 Δcdr1, avicel, 1 h 5 3
N. crassa SRR400636 ∆cdr1, avicel, 4 h 4 2
N. crassa SRR400637 ∆cdr1, sucrose, 1 h 5 3
N. crassa SRR400638 ∆cdr1, sucrose, 4 h 5 3
N. crassa SRR400639 ∆cdr2, avicel, 1 h 5 3
N. crassa SRR400640 ∆cdr2, avicel, 4 h 3 3
N. crassa SRR400641 ∆cdr2, sucrose, 1 h 5 3
N. crassa SRR400642 ∆cdr2, sucrose, 4 h 5 3
N. crassa SRR400643 wild type, avicel, 1 h 5 3
N. crassa SRR400644 wild type, avicel, 1 h 5 3
N. crassa SRR400645 wild type, avicel, 1 h 5 3
N. crassa SRR400646 wild type, avicel, 2 h 5 3
N. crassa SRR400647 wild type, avicel, 0.5 h 5 3
N. crassa SRR400648 wild type, avicel, 4 h 3 1
N. crassa SRR400649 wild type, avicel, 4 h 3 2
N. crassa SRR400650 wild type, avicel, 4 h 3 2
N. crassa SRR400651 wild type, no carbon, 1 h 5 2
N. crassa SRR400652 wild type, no carbon, 4 h 3 3
N. crassa SRR400653 wild type, no carbon, 4 h 2 2
N. crassa SRR400654 wild type, no carbon, 4 h 3 3
N. crassa SRR400655 wild type, sucrose, 1 h 3 2
N. crassa SRR400656 wild type, sucrose, 1 h 5 3
N. crassa SRR400657 wild type, sucrose, 1 h 5 3
N. crassa SRR400658 wild type, sucrose, 4 h 5 3
N. crassa SRR400659 wild type, sucrose, 4 h 5 3
N. crassa SRR400660 wild type, sucrose, 4 h 5 3
S. macrospora GSM832529 wild type vegetative mycelium 2 2
S. macrospora GSM832533 wild type vegetative mycelium 2 2
S. macrospora GSM832530 wild type sexual mycelium 3 1
S. macrospora GSM832534 wild type sexual mycelium 2 2
S. macrospora GSM832531 wild type protoperithecia 3 3
S. macrospora GSM832532 wild type protoperithecia 3 3
S. macrospora GSM832535 pro1 protoperithecia 3 2
S. macrospora GSM832536 pro1 protoperithecia 3 2
Eurotiomycetes    
A. flavus SRR283857 30°C 3 2
A. flavus SRR283858 37°C 4 3
A. oryzae SRR043191 solid culture 3 2
A. oryzae SRR035603 solid culture 3 2
A. oryzae SRR043192 liquid culture 4 3
A. oryzae SRR063693 liquid culture 3 2
A. oryzae SRR043193 solid culture ER stress 4 3
A. oryzae SRR065622 solid culture ER stress 3 3
A. oryzae SRR043194 liquid culture ER stress 4 3
A. oryzae SRR065623 liquid culture ER stress 3 2
Basidiomycota    
S. commune SRR065180 wild type 3 3
S. commune SRR065181 ∆hom2 3 3
S. commune SRR065182 ∆fst4 3 3
  1. ∆, Delta symbol denotes deletion mutants. For each analyzed sample, species and accession number are given. Data for P. confluens and S. macrospora were analyzed for expression distributions in previous studies with GEO accession numbers GSE41631 and GSE33668, respectively [11, 12]; the other datasets were analyzed in this study. For P. confluens, data from independent biological repetitions were subjected to a combined analysis, but results were similar to analyses of the individual datasets [12]. For all other analyses, data from individual RNA-seq experiments were used. RNA-seq data sets from the following studies were used for this analysis: Schizosaccharomyces pombe[18], Saccharomyces cerevisiae[14], Pyronema confluens[12], Tuber melanosporum[16], Neurospora crassa[13], Sordaria macrospora[11], Aspergillus flavus[19], Aspergillus oryzae[17], Schizophyllum commune[15]. More information on the studies and reference genomes used for mapping can be found in Additional file 1.
  2. 1proportion ≥ 0.15 (15%).
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