| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Monoclonal anti-VCP clone EPR3307(2) | Abcam | Cat# ab109240, RRID:AB_10862588 |
| Rabbit Polyclonal anti-SPP C-term | Abcam | ab190253 |
| Rabbit Monoclonal anti-Calnexin N-term clone EPR3632 | Abcam | Cat# ab92573, RRID:AB_10563673 |
| Rabbit Monoclonal anti-RNF185 clone EPR14070-94 | Abcam | ab181999 |
| Rabbit Monoclonal anti-Erlin2 clone EPR8089 | Abcam | Cat# ab128924, RRID:AB_11150974 |
| Rabbit Polyclonal anti-UBE3C | Abcam | ab226173 |
| Rabbit Monoclonal anti-TMUB1 clone EPR14066 | Abcam | ab180586 |
| Rabbit Polyclonal anti-SEL1L | Abcam | Cat# ab78298, RRID:AB_2285813 |
| Rabbit Monoclonal anti-BiP clone EPR4040(2) | Abcam | Cat# ab108613, RRID:AB_10859806 |
| Rabbit Polyclonal anti-Membralin/TMEM259 | Atlas Antibodies | Cat# HPA042669, RRID:AB_10794916 |
| Rabbit Polyclonal anti-TMEM41B | Atlas Antibodies | Cat# HPA014946, RRID:AB_2205037 |
| Mouse Monoclonal anti-VCP/p97 clone Clone18/VCP | BD Biosciences | Cat# 612183, RRID:AB_399554 |
| Rabbit Monoclonal anti-HRD1 clone D3O2A | Cell Signaling Technology | Cat# 14773, RRID:AB_2798607 |
| Rabbit Monoclonal anti-HIP2/UBE2K clone D27C4 | Cell Signaling Technology | Cat# 8226, RRID:AB_10827650 |
| Rabbit Polyclonal anti-Ub | Cell Signaling Technology | Cat# 3933, RRID:AB_2180538 |
| Rabbit Monoclonal anti-VMP1 clone D6N4G | Cell Signaling Technology | Cat# 12978, RRID:AB_2798077 |
| Rabbit Polyclonal anti-mNeonGreen | Cell Signaling Technology | Cat# 53061, RRID:AB_2799426 |
| Rabbit Polyclonal anti-LC3B | Cell Signaling Technology | Cat# 2775, RRID:AB_915950 |
| Rabbit Monoclonal anti-PDI clone C81H6 | Cell Signaling Technology | Cat# 3501, RRID:AB_2156433 |
| Mouse Monoclonal anti-CHOP clone L63F7 | Cell Signaling Technology | Cat# 2895, RRID:AB_2089254 |
| Rabbit Polyclonal anti-AMFR/gp78 | Cell Signaling Technology | Cat# 9590, RRID:AB_10860080 |
| Mouse Monoclonal anti-BAP31 clone A1/182 | Enzo Life Sciences | Cat# ALX-804-601-C100, RRID:AB_2050797 |
| Rabbit Polyclonal anti-TMUB2 | ProteinTech | 28044-1-AP |
| Rabbit Polyclonal anti-CYP51A1 | ProteinTech | Cat# 13431-1-AP, RRID:AB_2088571 |
| Mouse Monoclonal anti-GAPDH clone 1E6D9 | ProteinTech | Cat# 60004-1-Ig, RRID:AB_2107436 |
| Rabbit Polyclonal anti-CKAP4 (Climp63) | ProteinTech | Cat# 16686-1-AP, RRID:AB_2276275 |
| Rabbit Polyclonal anti-Erlin1 | ProteinTech | Cat# 17311-1-AP, RRID:AB_2098590 |
| Rat Monoclonal anti-HA clone 3F10 | Roche | Cat# 11867423001, RRID:AB_390918 |
| Rabbit Monoclonal anti-RNF5 clone 22B3 | Santa Cruz Biotechnology | Cat# sc-81716, RRID:AB_2238618 |
| Rat Monoclonal anti-Tubulin clone YOL1/34 | Santa Cruz Biotechnology | Cat# sc-53030, RRID:AB_2272440 |
| Mouse Monoclonal anti-FLAG-HRP clone M2 | Sigma-Aldrich | Cat# A8592, RRID:AB_439702 |
| Peroxidase AffiniPure F(ab’)2 Fragment Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | Labs Cat# 711-036-152, RRID:AB_2340590 |
| Peroxidase AffiniPure Donkey Anti-Rat IgG (H+L) | Jackson ImmunoResearch | Cat# 712-035-150, RRID:AB_2340638 |
| Peroxidase AffiniPure Donkey Anti-Mouse IgG (H+L) | Jackson ImmunoResearch | Cat# 715-035-150, RRID:AB_2340770 |
| Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, light chain specific | Jackson ImmunoResearch | Cat# 211-032-171, RRID:AB_2339149 |
| Peroxidase AffiniPure Goat Anti-Rat IgG, light chain specific | Jackson ImmunoResearch | Cat# 112-035-175, RRID:AB_2338140 |
| Peroxidase AffiniPure Goat Anti-Mouse IgG, light chain specific | Jackson ImmunoResearch | Cat# 115-035-174, RRID:AB_2338512 |
| Alexa Fluor 568 goat anti-mouse IgG (H+L) secondary antibody | Thermo Fisher Scientific | Cat# A-11004, RRID:AB_2534072 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DMEM medium | Sigma-Aldrich | Cat# D6429 |
| L-Glutamine (200 mM) | GIBCO (Thermo Fisher Scientific) | Cat# 25030024 |
| Penicillin-Streptomycin (10,000 U/mL) | GIBCO (Thermo Fisher Scientific) | Cat# 15140122 |
| 10% FBS | GIBCO (Thermo Fisher Scientific) | Cat# 26140079 |
| Zeocin | Invitrogen (Thermo Fisher Scientific) | Cat# R25001 |
| Puromycin | GIBCO (Thermo Fisher Scientific) | Cat# A1113803 |
| Tetracycline | Sigma-Aldrich | Cat# T7660 |
| Cycloheximide | Sigma-Aldrich | Cat# C7698 |
| TransIT LT1 | Mirus Bio LLC | Cat# MIR 2305 |
| OptiMEM | GIBCO (Thermo Fisher Scientific) | Cat# 31985062 |
| 3xFLAG peptide | Sigma-Aldrich | Cat# F4799 |
| cOmplete EDTA-free protease inhibitor cocktail | Roche | Cat# 5056489001 |
| Benzonase | Sigma-Aldrich | Cat# E1014 |
| N-Ethylmaleimide (NEM) | Sigma-Aldrich | Cat# E3876 |
| 1,4-Dithiothreitol (DTT) | Sigma-Aldrich | Cat# D9779 |
| PMSF | Roche | Cat# 11359061001 |
| Pepstatin A | Sigma-Aldrich | Cat# P5318 |
| DNase I | Roche | Cat# 11284932001 |
| DMNG | Anatrace | Cat# NG322 |
| DDM | Anatrace | Cat# D310 |
| CHS | Anatrace | Cat# CH210 |
| Tunicamycin | Cell Signaling Technology | Cat# 12819S |
| Thapsigargin | Cell Signaling Technology | Cat# 12758S |
| CB-5083 | Selleckchem | Cat# S8101 |
| dNTP mixture | Takara | Cat# 4030 |
| First Strand buffer | Invitrogen (Thermo Fisher Scientific) | Cat# 18080093 |
| RNaseOUT | Invitrogen (Thermo Fisher Scientific) | Cat# 10777019 |
| Fluoromount-G (with DAPI) | Invitrogen (Thermo Fisher Scientific) | Cat# 00-4959-52 |
| Critical Commercial Assays | ||
| FLAG-M2 Magnetic Beads | Sigma-Aldrich | Cat# M8823, RRID:AB_2637089 |
| Pierce Anti-HA Magnetic Beads | Thermo Fisher Scientific | Cat# 88837 |
| Pierce Streptavidin Magnetic Beads | Thermo Fisher Scientific | Cat# 88817 |
| mNeonGreen-Trap Magnetic Agarose | Chromotek | Cat# ntma-20 |
| QIAGEN BloodMaxi kit | QIAGEN | Cat# 51194 |
| QIAGEN BloodMini kit | QIAGEN | Cat# 51106 |
| NEBNext® Ultra II Q5® Master Mix | New England Biolabs | Cat# M0544L |
| SuperScriptIII | Invitrogen (Thermo Fisher Scientific) | Cat# 18080093 |
| SensiFAST SYBR® No-ROX kit | Bioline | Cat# BIO-98020 |
| Monarch® Total RNA Miniprep Kit | New England Biolabs | Cat# T2010S |
| Western Lightning ECL Pro | Perkin Elmer | Cat# NEL121001EA |
| Deposited Data | ||
| Genome-wide CRISPR-Cas9 screen | This study; ENA Data Set | Data S2; PRJEB37897 |
| Proteomics | This study; PRIDE Data Set | Data S3, S4, and S5; PXD018517 |
| Original western blot images | This study; Mendeley Data Set | https://doi.org/10.17632/ftrm9sc5m9.1 |
| Experimental Models: Cell Lines | ||
| Flp-In T-REx 293 Cell Line | Invitrogen (Thermo Fisher Scientific) | Cat# R78007 |
| Lenti-X 293T Cell Line | Clontech (Takara Bio) | Cat# 632180 |
| HeLa Cell Line | ATCC | ATCC® CCL-2 |
| Oligonucleotides | ||
| Focused sgRNA library targeting E2s and E3s | This study; (van de Weijer et al., 2017) | Data S1 |
| Z07 MBRL-mNeonGreen PCR tagging M1: GCTTCTGACACAACTCCCCTGGGGGC TGCGGTAGGCGGGCCTAGCCCGGCC TCCATGGCCCCAACGGAGGCGCCC TCGGAGGTGGGGTCCTCAGGTGGAG GAGGTAGTG |
Integrated DNA Technologies (IDT) | N/A |
| Z07 MBRL-mNeonGreen PCR tagging M2: GGCAGTCCCAGAGGAAGGA GGTGGCTGGCCTCCCCCACCCC CACGGGCTCGGGAAAAAAAACAG GCCCAGCCAGCAGGGGTATCTAC ACTTAGTAGAAATTAGCTAGCTG CATCGGTACC |
Integrated DNA Technologies (IDT) | N/A |
| Z07 HRD1-mNeonGreen PCR tagging M1: GGCACAGAGGAGATGCCTGA GGATGGAGAGCCCGATGCAGCAG AGCTCCGCCGGCGCCGCCTGCAG AAGCTGGAGTCTCCTGTTGCCC ACTCAGGTGGAGGAGGTAGTG |
Integrated DNA Technologies (IDT) | N/A |
| Z07 HRD1-mNeonGreen PCR tagging M2: TGTTCCAGCGAGGGCTGCTCAA AAGAGCAGAGGCTGGGGCTGGGCTG GGGCAGTGAAAAAAGCAGTGTCAGT GGGCAACAGATCTACACTTAGTAGA AATTAGCTAGCTGCATCGGTACC |
Integrated DNA Technologies (IDT) | N/A |
| OligodT-18-mer | Integrated DNA Technologies (IDT) | Cat# 51-01-15-07 |
| qPCR Human BiP primer pair: 5′-GGATCATCAACGAGCCTACG-3′ (forward); 5′-CACCCAGGTCAAAC ACCAG-3′ (reverse) |
Integrated DNA Technologies (IDT); | N/A |
| qPCR Human RNF185 primer pair: 5′-CTGTCACGCCTCTTCCTATTTGT-3′ (forward); 5′-GCCCAGCATTAG GCAATCAG-3′(reverse) |
Integrated DNA Technologies (IDT); (El Khouri et al., 2013) | N/A |
| qPCR Human MBRL primer pair: 5′-TCACTACCGCTTCAATGGGCAG-3′ (forward); 5′-CTGAAGCAGCA TCTCCTGGATG-3′(reverse) |
Integrated DNA Technologies (IDT); OriGene pre-design primers | N/A |
| qPCR Human CYP51A1 primer pair: 5′-CTACAGTCGCCTGACAACAC-3′ (forward); 5′-CCACTTTCTCC CCAACTCTC-3′ (reverse) |
Integrated DNA Technologies (IDT); (Sato et al., 2011) | N/A |
| qPCR Human GAPDH primer pair: 5′-AACCTGCCAAATATGATGAC-3′ (forward); 5′-AGGAAATGAGCT TGACAAAG-3′(reverse) |
Integrated DNA Technologies (IDT) | N/A |
| Recombinant DNA | ||
| pcDNA5-FRT-TO plasmid | Thermo Fisher Scientific | V652020 |
| Lentiviral cDNA expression vectors | (van de Weijer et al., 2014) | N/A |
| PCR-tagging plasmid Z07-mNeongreen | (Fueller et al., 2020) | Addgene Plasmid #124790 |
| Toronto KnockOut (TKO) CRISPR Library - Version 3 | (Hart et al., 2017) | Addgene #90294 |
| Software and Algorithms | ||
| MaxQuant, version 1.6.3.4 | MaxQuant | https://www.maxquant.org/ |
| Perseus software, version 1.5.5.3 | MaxQuant | https://maxquant.net/perseus/ |
| SlideBook 6 | 3i - Intelligent Imaging Innovations | https://www.intelligent-imaging.com/slidebook |
| Image studio software Li-Cor | Li-Cor | https://www.licor.com/bio/image-studio-lite/ |
| FlowJo 10.4 | FlowJo, LLC | https://www.flowjo.com/ |
| GraphPad Prism | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| MAGeCK | (Li et al., 2014) (Li et al., 2015) |
N/A |
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