Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Saccharomyces cerevisiae) | ALD5 | Saccharomyces Genome Database | SGD:S000000875 | |
| Gene (Saccharomyces cerevisiae) | GND2 | Saccharomyces Genome Database | SGD:S000003488 | |
| Gene (Saccharomyces cerevisiae) | PHO3 | Saccharomyces Genome Database | SGD:S000000296 | |
| Strain, strain background (Saccharomyces cerevisiae) | Oak; YJF153 | PMID:12702333 | YPS163 background | |
| Strain, strain background (Saccharomyces cerevisiae) | Wine; YJF1442 | PMID:16103919 | UCD2120 background | |
| Strain, strain background (Saccharomyces cerevisiae) | ChI; YJF1373 | PMID:22913817 | HN6 background | |
| Strain, strain background (Saccharomyces cerevisiae) | ChII; YJF1375 | PMID:22913817 | SX6 background | |
| Strain, strain background (Saccharomyces paradoxus) | YJF694 | PMID:19212322 | N17 background | |
| Strain, strain background (Saccharomyces uvarum) | YJF1450 | PMID:22384314 | CBS7001 background | |
| Recombinant DNA reagent | pIM202 | PMID:23921661 | CRE cloning vector | |
| Sequence-based reagent | S288c genome | PMID:22384314 | ||
| Sequence-based reagent | N17 genome | PMID:22384314 | ||
| Sequence-based reagent | CBS 7001 genome | PMID:22384314 | ||
| Sequence-based reagent | Oak genome | This paper | YJF153.fasta; YJF153.gff | https://doi.org/10.17605/OSF.IO/Y5748 |
| Sequence-based reagent | Wine genome | This paper | BC217.fasta; BC217.gff | https://doi.org/10.17605/OSF.IO/Y5748 |
| Sequence-based reagent | ChI genome | This paper | HN6.fasta; HN6.gff | https://doi.org/10.17605/OSF.IO/Y5748 |
| Sequence-based reagent | ChII genome | This paper | SX6.fasta; SX6.gff | https://doi.org/10.17605/OSF.IO/Y5748 |
| Sequence-based reagent | Intra-specific CRE-library | This paper | CRE_Libraries.YJF1455.csv | https://doi.org/10.17605/OSF.IO/Y5748 |
| Sequence-based reagent | Inter-specific CRE-library | This paper | CRE_Libraries.YJF1484.csv | https://doi.org/10.17605/OSF.IO/Y5748 |
| Commercial assay or kit | Dynabeads mRNA Direct kit | Invitrogen | Invitrogen:61011 | |
| Commercial assay or kit | YeaStar DNA kit | Zymo Research | Zymo:D2002 | |
| Commercial assay or kit | YeaStar RNA kit | Zymo Research | Zymo:R1002 | |
| Commercial assay or kit | Dynabeads mRNA Direct kit | Zymo Research | Zymo:D2002 | |
| Commercial assay or kit | Glucose (GO) Assay Kit | Sigma | Sigma:GAGO20 | |
| Software, algorithm | BWA v0.7.5 | PMID:19451168 | RRID:SCR_010910 | https://github.com/lh3/bwa |
| Software, algorithm | PicardTools v1.114 | Broad Institute | RRID:SCR_006525 | https://github.com/broadinstitute/picard |
| Software, algorithm | GATK HaplotypeCaller v3.3–0 | Broad Institute | RRID:SCR_001876 | https://github.com/broadinstitute/gatk/ |
| Software, algorithm | liftOver | UCSC Genome Browser | RRID:SCR_018160 | https://genome-store.ucsc.edu/ |
| Software, algorithm | Fastx-toolkit | Hannon Lab | RRID:SCR_005534 | https://github.com/agordon/fastx_toolkit |
| Software, algorithm | Bowtie2 v2.1.0 | PMID:22388286 | RRID:SCR_016368 | https://github.com/BenLangmead/bowtie2 |
| Software, algorithm | Htseq-count | PMID:25260700 | RRID:SCR_011867 | https://github.com/htseq/htseq |
| Software, algorithm | DESeq2 | PMID:25516281 | RRID:SCR_015687 | https://doi.org/10.18129/B9.bioc.DESeq2 |
| Software, algorithm | Patser | PMID:10487864 | http://stormo.wustl.edu/software.html | |
| Software, algorithm | Custom R scripts | This paper | https://doi.org/10.17605/OSF.IO/Y5748 |