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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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BMC Research Notes

ISSN: 1756-0500

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