KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | ||
| Acid phenol chloroform | Ambion | AM9722 |
| Phenol chloroform isoamyl alcohol | Ambion | AM9732 |
|
Critical Commercial Assays | ||
| MEGAclear transcription clean-up kit | Ambion | AM1908 |
| NEB DNase I | New England Biolabs | M0303 |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumina | New England Biolabs | E7420 |
| NEBNext Poly(A) mRNA Magnetic Isolation Module | New England Biolabs | E7490 |
| NEBNext Multiplex Oligos for Illumina | New England Biolabs | E7335, E7500 |
| High sensitivity DNA kit for Bioanalyzer | Agilent | 5067-4626 |
| Library quantification kit | KAPA Biosystems | KK4824 |
| Fluorometric chitinase activity kit | Sigma-Aldrich | CS1030 |
|
Deposited Data | ||
| RNA-Seq data | this study | GEO: GSE150855 |
| Card-See data | this study | GEO: GSE150856 |
|
Experimental Models: Organisms/Strains | ||
| Mouse: BALB/c | Charles River Laboratories | Stock No: 028 |
| SN152 | Noble et al. Euk Cell 2005 | leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN235 | this study | leu2Δleu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN250 | Noble et al. Euk Cell 2005 | leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN425 | Noble et al. Euk Cell 2005 | leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ::C.d.ARG4, iro1Δ/IRO1, MTLa/α |
| SN1011 | Homann et al. 2009 | efg1Δ::ST8-C.m.LEU2/efg1Δ::ST8-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1338 | this study | efg1Δ::ST8-C.m.LEU2/efg1Δ::ST8-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4::ST61-C.d.ARG4Δ, iro1Δ/IRO1, MTLa/α |
| SN1351 | this study | wor1Δ::ST63-C.m.LEU2/wor1Δ::ST15-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1352 | this study | wor1Δ::ST63-C.m.LEU2/wor1Δ::ST15-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1142 | Homann et al. 2009 | wor2Δ::ST27-C.m.LEU2/wor2Δ::ST27-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1143 | Homann et al. 2009 | wor2Δ::ST27-C.m.LEU2/wor2Δ::ST27-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1111 | this study | wor3Δ::C.m.LEU2/wor3Δ::C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1433 | this study | wor3Δ::C.m.LEU2/wor3Δ::ST35-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1493 | this study | wor4Δ::ST67-C.m.LEU2/wor4Δ::ST5-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1494 | this study | wor4Δ::ST67-C.m.LEU2/wor4Δ::ST6-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1144 | Homann et al. 2009 | czf1Δ::ST42-C.m.LEU2/czf1Δ::ST42-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1145 | Homann et al. 2009 | czf1Δ::ST42-C.m.LEU2/czf1Δ::ST42-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1187 | Homann et al. 2009 | ahr1Δ::ST42-C.m.LEU2/ahr1Δ::ST42-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1188 | Homann et al. 2009 | ahr1Δ::ST45-C.m.LEU2/ahr1Δ::ST45-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1488 | this study | ssn6Δ::C.m.LEU2/ssn6Δ::ST18-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN928 | Pande et al 2013 | SAT1-PTDH3-WOR1/wor1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1448 | this study | SAT1-PTDH3-WOR1/wor1Δ::C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1507 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR1/wor1Δ::C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1045 | Pande et al 2013 | SAT1-PTDH3-WOR1/wor1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α (mouse passage) |
| SN1465 | this study | SAT1-PTDH3-WOR1/wor1Δ::C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α (mouse passage) |
| SN1251 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR2/wor2Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1245 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR3/wor3Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1533 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR4/wor4Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1447 | this study | FRT-FLP-SAT1-FRT-PTDH3-CZF1/czf1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1445 | this study | FRT-FLP-SAT1-FRT-PTDH3-CZF1/czf1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1522 | this study | FRT-FLP-SAT1-FRT-PTDH3-AHR1/ahr1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1525 | this study | FRT-FLP-SAT1-FRT-PTDH3-AHR1/ahr1Δ::C.d.ARG4, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1126 | this study | efg1Δ::C.m.LEU2/efg1Δ::C.d.HIS1, wor1Δ::C.d.ARG4/wor1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1373 | this study | efg1Δ::C.m.LEU2/efg1Δ::C.d.HIS1, czf1Δ::C.d.ARG4/czf1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1341 | this study | wor3Δ::C.m.LEU2/wor3Δ::C.d.HIS1, wor1Δ::C.d.ARG4/wor1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1377 | this study | wor3Δ::C.m.LEU2/wor3Δ::C.d.HIS1, czf1Δ::C.d.ARG4/czf1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1340 | this study | wor2Δ::C.m.LEU2/wor2Δ::C.d.HIS1, wor1Δ::C.d.ARG4/wor1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1375 | this study | wor2Δ::C.m.LEU2/wor2Δ::C.d.HIS1, czf1Δ::C.d.ARG4/czf1Δ::FRT-FLP-SAT1-FRT, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1245 | this study | wor3Δ::C.m.LEU2/wor3Δ::C.d.HIS1, FRT-FLP-SAT1-FRT-PTDH3-WOR2/wor2Δ::C.d.ARG4, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1656 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR1/wor1Δ::C.m.LEU2, FRT-PTDH3-WOR2/wor2Δ::C.d.HIS1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1657 | this study | FRT-FLP-SAT1-FRT-PTDH3-WOR1/wor1Δ::C.m.LEU2, FRT-PTDH3-WOR2/wor2Δ::C.d.HIS1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1147 | this study | SAT1-PTDH3-WOR1/wor1Δ::C.d.ARG4, czf1Δ::C.m.LEU2/czf1Δ::C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1468 | this study | SAT1-PTDH3-WOR1/wor1Δ::C.d.HIS1, czf1Δ::C.m.LEU2/czf1Δ::C.d.ARG4, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1873 | this study | leu2Δ:: 5′ UTR homology-split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1877 | this study | leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.m.LEU2-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1903 | this study | leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.m.LEU2-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′, TDH3/tdh3::P_TDH3-C.a.PBASE-FRT-FLP-SAT1-FRT |
| SN1933 | this study | leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.m.LEU2-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′, WOR1-PBASE-FRT/WOR1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2012 | this study | leu2Δ:: 5′ UTR homology-split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ efg1Δ::PBASE-FRT/EFG1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1988 | this study | leu2Δ:: 5′ UTR homology-split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ, EFG1-PBASE-FRT/EFG1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1943 | this study | leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.m.LEU2-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′ EFG1-PBASE-FRT/EFG1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN1941 | this study | leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.d.HIS1-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′/leu2Δ::split C.d.ARG4 3′-PiggyBac transposon LTR-C.m.LEU2-multiplex PE primer 2-PiggyBac transposon LTR-split C.d.ARG4 5′ CZF1-PBASE-FRT/CZF1 leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2157 | this study | cht2Δ::ST94-C.m.LEU2/cht2Δ::ST46-C.d.HIS1, leu2Δ/leu2Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2161 | this study | cht2Δ::FRT-FLP-SAT1-FRT/cht2Δ::FRT-FLP-SAT1-FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2162 | this study | cht2Δ::FRT/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2170 | this study | CHT2/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2172 | this study | CHT2 D151A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2174 | this study | CHT2 E153A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2175 | this study | CHT2 D151A,E153A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2178 | this study | CHT2 Y211A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2180 | this study | CHT2 W278A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2225 | this study | CHT2/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ::ST4-C.d. ARG4/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2227 | this study | CHT2 D151A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ::ST3-C.d. ARG4/arg4Δ, iro1Δ/IRO1, MTLa/α |
| SN2230 | this study | CHT2 D151A,E153A/cht2Δ::FRT, leu2Δ::C.m.LEU2/leu2::C.d.HIS1Δ, ura3Δ/URA3, his1Δ/his1Δ, arg4Δ::ST1-C.d. ARG4/arg4Δ, iro1Δ/IRO1, MTLa/α |
|
Oligonucleotides | ||
| Oligonucleotides are described in Table S6 | N/A | N/A |
|
Recombinant DNA | ||
| pSFS2A | ||
| pSN42 | Noble et al. 2005 | Gene replacement with LEU2 marker |
| pSN52 | Noble et al. 2005 | Gene replacement with HIS1 marker |
| pSN69 | Noble et al. 2005 | Gene replacement with ARG4 marker |
| pSN209 | Pande et al. 2013 | Replacement of WOR1 promoter with (SAT1 gene and) TDH3 promoter |
| pSN377 | this study | Replacement of WOR1 promoter with (Flipper cassette and) TDH3 promoter |
| pSN301 | this study | Replacement of WOR1 ORF with FLP-SAT1 construct |
| pSN314 | this study | Replacement of WOR2 promoter with (Flipper cassette and) TDH3 promoter |
| pSN311 | this study | Replacement of WOR3 promoter with (Flipper cassette and) TDH3 promoter |
| pSN360 | this study | Replacement of WOR4 promoter with (Flipper cassette and) TDH3 promoter |
| pSN352 | this study | Replacement of CZF1 promoter with (Flipper cassette and) TDH3 promoter |
| pSN329 | this study | Replacement of CZF1 ORF with FLP-SAT1 construct |
| pSN378 | this study | Replacement of AHR1 promoter with (Flipper cassette and) TDH3 promoter |
| pSN445 | this study | Transposon integration into C.a.LEU2 locus |
| pSN447 | this study | Transposon integration into C.a.LEU2 locus |
| pSN427 | this study | Plasmid that can be used to create additional plasmids with gene homology for TF-PiggyBac transposase fusions |
| pSN422 | this study | Replacement of TDH3 ORF with PiggyBac transposase for overexpression |
| pSN459 | this study | Fusion of PiggyBac transposase to WOR1 ORF |
| pSN467 | this study | Fusion of PiggyBac transposase to EFG1 ORF |
| pSN465 | this study | Fusion of PiggyBac transposase to CZF1 ORF |
| pSN503 | this study | CHT2 allele B addbback to endogenous locus |
| pSN504 | this study | CHT2 allele B D151A addbback to endogenous locus |
| pSN505 | this study | CHT2 allele B E153A addbback to endogenous locus |
| pSN506 | this study | CHT2 allele B D151A,E153A addbback to endogenous locus |
| pSN507 | this study | CHT2 allele B Y211A addbback to endogenous locus |
| pSN508 | this study | CHT2 allele B W278A addbback to endogenous locus |
|
Software and Algorithms | ||
| NumPy 1.14.3 | Oliphant, 2015 | RRID: SCR_008633 |
| Pandas | Reback et al., 2021 | RRID:SCR_018214 |
| SciPy | Virtanen et al., 2020 | RRID:SCR_008058 |
| tabulate | Astanin et al., 2021 | https://pypi.org/project/tabulate/ |
| pybedtools | Dale et al., 2011 | RRID:SCR_021018 |
| BedTools | Quinlan and Hall, 2010 | RRID:SCR_006646 |
| Picard | http://broadinstitute.github.io/picard/ | RRID:SCR_006525 |
| Htslib | Li et al., 2009 | RRID:SCR_002105 |
| samtools | Li et al., 2009 | RRID:SCR_002105 |
| Pysam | https://github.com/pysam-developers/pysam | RRID:SCR_021017 |
| Kallisto | Bray et al., 2016 | RRID:SCR_016582 |
| Limma | Ritchie et al., 2015 | RRID:SCR_010943 |
| Bowtie | Langmead and Salzberg., 2012 | RRID:SCR_005476 |
| MochiView | Homann and Johnson, 2010 | RRID:SCR_000259 |
| Custom code for Calling Card analysis in Candida albicans | this study | https://github.com/jwitch/CallingCard |
|
Other | ||
| Sera-Mag beads in a homemade PEG solution | Thermo-Fisher | (https://openwetware.org/wiki/SPRI_bead_mix) |