Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (S. cerevisiae, BY4741) | Ccr4_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000000019 | |
| Strain, strain background (S. cerevisiae, BY4741) | Pop2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005335 | |
| Strain, strain background (S. cerevisiae, BY4741) | Not1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000000689 | |
| Strain, strain background (S. cerevisiae, BY4741) | Caf40_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005232 | |
| Strain, strain background (S. cerevisiae, BY4741) | Pan2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000003062 | |
| Strain, strain background (S. cerevisiae, BY4741) | Pan3_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000001508 | |
| Strain, strain background (S. cerevisiae, BY4741) | Dcp1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005509 | |
| Strain, strain background (S. cerevisiae, BY4741) | Dcp2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005062 | |
| Strain, strain background (S. cerevisiae, BY4741) | Edc2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000000837 | |
| Strain, strain background (S. cerevisiae, BY4741) | Edc3_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000000741 | |
| Strain, strain background (S. cerevisiae, BY4741) | Dhh1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000002319 | |
| Strain, strain background (S. cerevisiae, BY4741) | Xrn1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000003141 | |
| Strain, strain background (S. cerevisiae, BY4741) | Rrp6_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005527 | |
| Strain, strain background (S. cerevisiae, BY4741) | Csl4_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005176 | |
| Strain, strain background (S. cerevisiae, BY4741) | Rrp40-TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005502 | |
| Strain, strain background (S. cerevisiae, BY4741) | Rrp4_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000001111 | |
| Strain, strain background (S. cerevisiae, BY4741) | Rrp44_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005381 | |
| Strain, strain background (S. cerevisiae, BY4741) | Air1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000001341 | |
| Strain, strain background (S. cerevisiae, BY4741) | Trf5_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005243 | |
| Strain, strain background (S. cerevisiae, BY4741) | Mtr4_TAP | C-terminally tagged gene (Open Biosystems, Germany). |
SGD: S000003586 | |
| Strain, strain background (S. cerevisiae, BY4741) | Air2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000002334 | |
| Strain, strain background (S. cerevisiae, BY4741) | Trf4_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005475 | |
| Strain, strain background (S. cerevisiae, BY4741) |
Ski2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000004390 | |
| Strain, strain background (S. cerevisiae, BY4741) | Ski3_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000006393 | |
| Strain, strain background (S. cerevisiae, BY4741) | Ski7_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000005602 | |
| Strain, strain background (S. cerevisiae, BY4741) | Ski8_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000003181 | |
| Strain, strain background (S. cerevisiae, BY4741) | Upf1_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000004685 | |
| Strain, strain background (S. cerevisiae, BY4741) | Upf2_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000001119 | |
| Strain, strain background (S. cerevisiae, BY4741) | Upf3_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000003304 | |
| Strain, strain background (S. cerevisiae, BY4741) | Nmd4_TAP | C-terminally tagged gene (Open Biosystems, Germany). | SGD: S000004355 | |
| Antibody | IgG | Sigma-Aldrich | Cat#: I5006, RRID:AB_1163659 | IP: 0.1 mg per IP |
| Antibody | PAP anti-TAP | Sigma Aldrich | Cat#: P1291, RRID:AB_1079562 | WB (1:2000) |
| Commercial assay or kit | Dynabeads Protein G | Invitrogen | Cat#: 10003D | 330 µl per IP |
| Commercial assay or kit | RNase T1 | Thermo Fisher Scientific | Cat#: EN0541 | |
| Commercial assay or kit | Antarctic Phosphatase | NEB | Cat#: M0289S | |
| Commercial assay or kit |
RNase OUT | Invitrogen | Cat#: 10777019 | |
| Commercial assay or kit | T4 Polynucleotide Kinase | Invitrogen | Cat#: EK0032 | |
| Commercial assay or kit | T4 RNA ligase 2, truncated KQ | NEB | Cat#: M0373S | |
| Commercial assay or kit | T4 RNA ligase 1 | NEB | Cat#: M0437M | |
| Commercial assay or kit | Proteinase K | NEB | Cat#: P8107S | |
| Commercial assay or kit | SuperScript III RT | Thermo Fisher Scientific | Cat#: 18080093 | |
| Commercial assay or kit |
Phusion High-Fidelity PCR Master Mix |
Thermo Fisher Scientific | Cat#: F531S | |
| Chemical compound, drug | 4-thiouracil | Carbosynth | Cat#: 591-28-6 |
1 mM final conc. |
| Software, algorithm | mockinbird | Roth and Torkler, 2018;https://github.com/soedinglab/Degradation_scripts | ||
| Software, algorithm | UMI-tools | Smith et al., 2017; doi:10.1101/gr.209601.116 | ||
| Software, algorithm | Skewer | Jiang et al., 2014; doi: 10.1186/1471-2105-15-182 | ||
| Software, algorithm | Bowtie | Langmead et al., 2009; doi: 10.1186/gb-2009-10-3-r25 | ||
| Software, algorithm | tSNE | Van Der Maaten and Hinton, 2008; doi: 10.1007/s10479-011-0841-3 |