KEY RESOURCES TABLE
| REAGENT or RESOURCE |
SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-HA | Sigma-Aldrich | 11583816001 |
| Mouse monoclonal anti-GFP | Sigma-Aldrich | 11814460001 |
| Rabbit IgG | Sigma-Aldrich | I5006 |
| Anti-mouse HRP | Abcam | ab6728 |
| Nanobody Anti-GFP | Rothbauer et al., 2008 | GBP |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Rapamycin | Bio Basic | R706203 |
| Indole-3-acetic acid (IAA/Auxin) | Sigma-Aldrich | I3750 |
| 1-6 Hexanediol | Sigma-Aldrich | H11807 |
| Dynabeads M-270 Epoxy | Invitrogen | 14302D |
| RNAsin | Promega | N2111 |
| Pepstatin A | Sigma-Aldrich | P5318 |
| PMSF | Sigma-Aldrich | P7626 |
| antifoam | Sigma-Aldrich | A5633 |
| Glutaraldehyde | Sigma-Aldrich | G6257 |
| Trypsin Protease | Promega | V511A |
| Phusion DNA polymerase | ThermoFischer | F630S |
| Q5 DNA polymerase | NEB | M0491L |
| YPD | Biobasic | SD7022 |
| Yeast nitrogen base w/o amino acids | Biobasic | S505 |
| Concanavalin A | Sigma-Aldrich | C5275 |
| Halo-ligand JF-549 | Luke Lavis, Janelia Research Campus | Grimm et al., 2015 |
| Trizol | Invitrogen | 15596026 |
| Ultra-pure water | Invitrogen | 10977023 |
| Critical Commercial Assays | ||
| QIAquick PCR purification kit | Biobasic | BS664 |
| Direct-zol Miniprep Kit | Zymo research | R2050 |
| Deposited data | ||
| NPC affinity purification and Mass spectrometry | This manuscript. | Project Name: Nuclear pore complexes interactome dissection PRIDE Project DOI: 10.6019/PXD027872 |
| NPC-AP-RNAseq | This manuscript. | GEO: GSM5492330 |
| RNA poly(A) tail sequencing | Tudek et al., 2021 | https://doi.org/10.17632/v5vm3dmm8y.1. |
| Raw data files | This study | Mendeley, DOI: 10.17632/krwndnhw87.1 |
| Experimental model: Cell lines | ||
| Saccharomyces cerevisiae: W303-1A and W303-1B | Laboratory of Rodney Rothstein | ATCC:208352 ATCC:201238 |
| Yeast strains used | This manuscript. | Supplemental Table S1 |
| Oligonucleotides | ||
| Oligonucleotides used | This manuscript. | Supplemental Table S3 |
| Recombinant DNA | ||
| Plasmids used | This manuscript. | Supplemental Table S2 |
| Software and Algorithms | ||
| FIJI – Open source edition | ImageJ | http://fiji.sc; RRID:SCR_002285 |
| ZEN Microscopy software | Zeiss | Version ZEN 2012 SP5 |
| Scaffold (version 4.8.4) | Proteome Software, Inc., Portland, OR | https://www.proteomesoftware.com/ |
| RNA-seq analysis code | This manuscript. | Zenodo, DOI: 10.5281/zenodo.7063132 |
| Figures | This manuscript. | BioRender.com |
| RNA-seq analysis | Trimmomatic (version 0.38.0) | https://toolshed.g2.bx.psu.edu/repository?repository_id=ef9e620e9ac844b3 |
| RNA-seq analysis | STAR (version 2.5.2a) | https://toolshed.g2.bx.psu.edu/repository?repository_id=b8c12e1910b4735a |
| RNA-seq analysis | Htseq-count (version 0.11.3) | https://toolshed.g2.bx.psu.edu/repository?repository_id=2df7e24ce6c1f224 |