Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (S. cerevisiae) | WT; prototroph | Tsukiyama Lab | YTT5781 | MATa RAD5+ |
| Strain, strain background (S. cerevisiae) | WT; prototroph | Tsukiyama Lab | YTT5782 | MATa RAD5+ |
| Strain, strain background (S. cerevisiae) | Sth1 and Sfh1 degrons | Tsukiyama Lab | YTT7222 | MATa can1-100 RAD5 + Sth1-3HSV-IAA1-T10-KanMX Sfh1-3HSV-IAA1-T10-Hyg |
| Strain, strain background (S. cerevisiae) | Sth1 and Sfh1 degrons | Tsukiyama Lab | YTT7224 | MATa can1-100 RAD5 + Sth1-3HSV-IAA1-T10-KanMX Sfh1-3HSV-IAA1-T10-Hyg |
| Strain, strain background (S. cerevisiae) | dst1∆ | Tsukiyama Lab | YTT7308 | MATa RAD5 + dst1∆::KanMX |
| Strain, strain background (S. cerevisiae) | dst1∆ | Tsukiyama Lab | YTT7309 | MATa RAD5 + dst1∆::KanMX |
| Chemical compound, drug | Indole-3-acetic acid (IAA) | Sigma | I3750-5G-A | 1 mg/mL powder added to culture |
| Antibody | Rpb3 (mouse monoclonal) | Biolegend | 665003 | WB: (1:1000) dilution ChIP: (2 μL) |
| Antibody | Ser5p (rat monoclonal) | Active Motif | 61085 | WB: (1:1000) |
| Antibody | Ser2p (rat monoclonal) | Active Motif | 61083 | WB: (1:1000) |
| Antibody | HSV (rabbit polyclonal) | Sigma | H6030-200UG | WB: (1:5000) |
| Antibody | H3 (rabbit polyclonal) | Abcam | 1791 | WB: (1:1000) ChIP: (1 μL) |
| Antibody | Flag (mouse monoclonal) | Sigma | F1804 | ChIP: (2 μL) |
| Other | Protein G magnetic | Invitrogen | 10004D | ChIP: (20 μL) |
| Peptide, recombinant protein | Zymolyase 100T | AMSBIO | 120493–1 | MNase-seq; 10 mg per 100 units OD660 cells |
| Peptide, recombinant protein | Micrococcal nuclease | Worthington | LS004798 | MNase-seq 50U (high digests) 5U (low digests) |
| Other | AMPure XP | Beckman | A63880 | - |
| Strain, strain background (K. lactis) |
Spike-in control strain | Nathan Clark Lab | NRRL Y-1140 | 100:1 cell mixture (S. cerevisiae: K. lactis) |
| Chemical compound, drug | 4-Thiouracil | Sigma | 440736–1G | 5 mM |
| Commercial assay or kit | RiboPure Yeast Kit | Thermo Fisher | AM1926 | |
| Chemical compound, drug | MTSEA biotin-XX | Biotium | 90066 | 16.4 μM in 20 mM HEPES pH 7.4 1 mM EDTA |
| Other | Streptavidin beads | Invitrogen | 65001 | (40 μL) |
| Commercial assay or kit | miRNeasy kit | Qiagen | 217084 | - |
| Commercial assay or kit | Ovation SoLo kit; custom AnyDeplete | NuGEN/Tecan | Contact rep for custom reagent (yeast rRNA depletion) | - |