| Antibodies |
|
|
|
| Anti-FRQ (rabbit) |
Jay Dunlap (Garceau et al., 1997) |
N/A |
|
| Bacterial and Virus Strains |
|
|
|
| E.coli, DH5alpha, Electro-competent |
New England Bio |
C2989K |
|
| Chemicals, Peptides, and Recombinant Proteins |
|
|
|
| USB TPCK treated Trypsin |
Affymetrix |
22725 250 MG |
| Protease Inhibitor Cocktail |
Sigma |
P9599 |
| Protease Inhibitor Cocktail |
ThermoScientific |
1861282 |
| SuperSignal West Femto ECL (Pierce) |
ThermoFisher |
34094 |
| NADPH Tetrasodium salt (Roche) |
Sigma |
NADPH-RO |
| D-(+)-Xylose, ≥99% |
Sigma |
X1500–500G |
|
| Critical Commercial Assays |
|
|
|
| BCA protein quantification kit (Pierce) |
ThermoFisher |
23225 |
| TMT10plex Isobaric Mass Tag Labeling Reagents Sets |
ThermoFisher |
90406 |
|
| Deposited Data |
|
|
|
| Mass spectrometry proteomics data: ProteomeXchange Consortium via the PRIDE partner repository |
This paper |
PXD009682 and 10.6019/PXD009682 |
| RNA-seq data: National Center for Biotechnology Information Short Read Archive (SRA) |
Hurley et al. (2014) |
SRP045821 and SRP046458 |
| Mendeley dataset: Raw and processed TMT-MS and RNA-seq data. |
This paper |
[https://doi.org/10.17632/8mzwdr9sxc.1] |
| Mendeley dataset: Genes sets used for FunCat analyses. |
This paper |
[https://doi.org/10.17632/r68j3rnxhw.1] |
| Mendeley dataset: Raw XR enzyme activity assay data. |
This paper |
[https://doi.org/10.17632/x3c66jk53m.1] |
|
| Experimental Models: Organisms/Strains |
|
|
|
|
S. cerevisiae: FY834 |
Fungal Genetics Stock Left (Colot et al., 2006) |
FGSC #9721 |
|
N. crassa: WT: 74-OR23–1VA
|
Fungal Genetics Stock Left |
FGSC #2489 |
|
N. crassa: Δcsp-1: delta csp-1::hph+ |
Fungal Genetics Stock Left |
FGSC #11348 |
|
N. crassa: FGSC9718: delta mus-51::bar+ |
Fungal Genetics Stock Left |
FGSC #9718 |
|
N. crassa: 536–1: frhV5H6::bar+;ras-1bd
|
Jen Hurley (Hurley et al., 2013) |
536 |
|
N. crassa: Pfrq:luc: Pfrq(c-box)::luc::hph+ |
Jay Dunlap |
WT-1 |
|
N. crassa: XR:LUC: XR::luc::hph+ |
This paper |
Clones #4, 5, 10 |
|
| Oligonucleotides |
|
|
|
| Primer: pRS426 to NCU08384, -1000 bp from stop codon, forward: GTAACGCCAGGGTTTTCCCAGTCACGAC/ ATTTTAAGGACACGAGGAGCAG |
This paper |
SFQ7 |
| Primer: NCU08384 (end of ORF minus stop codon) to luciferase/hph,forward: GAGAACCTCTGGATTTTCGGT/ GGCGGAGGCGGCGGAGGCGG |
This paper |
SFQ8 |
| Primer: NCU08384 (end of ORF minus stop codon) to luciferase/hph,reverse: CCGCCTCCGCCGCCTCCGCC/ ACCGAAAATCCAGAGGTTCTC |
This paper |
SFQ9 |
| Primer: Luciferase/hph to NCU08384, just after stop codon, forward: GAAGTTATGGATCCGAGCTCG/ GTCAACCTTTTTCCGCAGCTTAG |
This paper |
SFQ10 |
| Primer: Luciferase/hph to NCU08384, just after stop codon, reverse: CTAAGCTGCGGAAAAAGGTTGAC/ CGAGCTCGGATCCATAACTTC |
This paper |
SFQ11 |
| Primer: NCU08384, +1000 bp from stop codon to pRS426, reverse: GCGGATAACAATTTCACACAGGAAACAGC/ GCCGGCATTGTATAGGAACAAG |
This paper |
SFQ12 |
|
| Recombinant DNA |
|
|
|
| Plasmid: pRS426: Yeast episomal vector with URA3 marker, and Ampicillin resistance |
Fungal Genetics Stock Left (Colot et al., 2006) |
pRS426 |
|
| Software and Algorithms |
|
|
|
| LIMBR v. “pre-alpha”, Oct 3, 2016 |
Crowell et al. (2018) |
https://github.com/aleccrowell/LIMBR |
| eJTK_cycle, v. Aug 3, 2016 |
Hutchison et al. (2015); Hutchison et al. (2018)
|
https://github.com/alanlhutchison/empirical-JTK_CYCLE-with-asymmetry |
| FunCat v. 8/12/2010, within FungiFun v. 0.5 |
Priebe et al. (2011) |
https://elbe.hki-jena.de/fungifun/ |
| PSEA, v. 1.1 |
Zhang et al. (2016) |
https://github.com/ranafi/PSEA |
| Pathway Tools software within the BioCyc Pathway/ Genome Database (PGDB), v. 21.5 |
Caspi et al. (2016) |
https://biocyc.org/ |
| Toolset Image Analysis Larrondo’s Lab v. 1.0, within FIJI (ImageJ) v. 2.0.0 |
Jen Hurley (Larrondo et al., 2012; Schindelin et al., 2012) |
https://fiji.sc/ |
