Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (human) | HEK293T | ATCC | Cat# CRL-3216; RRID:CVCL_0063 |
|
| Cell line (human) | K562 | ATCC | Cat# CCL-243; RRID:CVCL_0004 |
|
| Cell line (human) | HeLa | Hein et al., 2015 | RRID:CVCL_1922 | |
| Antibody | Anti-V5 (Mouse monoclonal) | Invitrogen | Cat# R960; RRID:AB_2556564 |
Immunofluorescence (1:1000) |
| Antibody | Anti-TOMM20 (Rabbit monoclonal) | Abcam | Cat# ab186735; RRID:AB_2889972 |
Immunofluorescence (1:500) |
| Antibody | Anti-GRASP65 (Mouse monoclonal) | Santa Cruz | Cat# sc-374423; RRID:AB_10991322 |
Immunofluorescence (1:500) |
| Antibody | Anti-CANX (Rabbit polyclonal) | Thermo Fisher | Cat# PA5-34754; RRID:AB_2552106 |
Immunofluorescence (1:500) |
| Antibody | Anti-PEX14 (Rabbit polyclonal) | Proteintech | Cat# 10594-1-AP; RRID:AB_2252194 |
Immunofluorescence (1:500) |
| Antibody | Anti-RCN2 (Rabbit polyclonal) | Thermo Fisher | Cat# PA5-56542; RRID:AB_2646431 |
Immunofluorescence (1:500) |
| Antibody | Anti-GAPDH (Mouse monoclonal) | Santa Cruz | Cat# sc-32233; RRID:AB_627679 |
Western blot (1:4500) |
| Antibody | Anti-SAE1 (Rabbit polyclonal) | Sigma | Cat# SAB4500028; RRID:AB_10742679 |
Western blot (1:500) |
| Antibody | Anti-COX4 (Rabbit polyclonal) | Abcam | Cat# ab16056; RRID:AB_443304 |
Western blot (1:1000) |
| Antibody | Anti-VDAC1 (Mouse monoclonal) | Abcam | Cat# ab14734; RRID:AB_443084 |
Western blot (1:500) |
| Antibody | Anti-AKAP1 (Mouse monoclonal) | Santa Cruz | Cat# sc-135824; RRID:AB_2225573 |
Immunofluorescence (1:200); western blot (1:500) |
| Antibody | Anti-MAVS (Mouse monoclonal) | Santa Cruz | Cat# sc-166583; RRID:AB_2012300 |
Immunofluorescence (1:200); western blot (1:250) |
| Antibody | Anti-SYNJ2BP (Rabbit polyclonal) | Sigma | Cat# HPA000866; RRID:AB_2276678 |
Western blot (1:500) |
| Antibody | Anti-FIS1 (Rabbit polyclonal) | Thermo Fisher | Cat# 10956–1-AP; RRID:AB_2102532 |
Western blot (1:1000) |
| Antibody | Anti-EMC4 (Rabbit monoclonal) | Abcam | Cat# ab184162; RRID:AB_2801471 |
Western blot (1:1000) |
| Antibody | Anti-EMC10 (Rabbit monoclonal) | Abcam | Cat# ab180148; RRID:AB_2889936 |
Western blot (1:500) |
| Antibody | Anti-CALR (Rabbit polyclonal) | Thermo Fisher | Cat# PA3900; RRID:AB_325990 |
Western blot (1:500) |
| Antibody | Anti-VTI1B (Rabbit monoclonal) | Abcam | Cat# ab184170; RRID:AB_2889935 | Western blot (1:250) |
| Antibody | Anti-SQS (Rabbit monoclonal) | Abcam | Cat# ab195046; RRID:AB_2860018 |
Western blot (1:500) |
| Antibody | Anti-Mouse Alexa Fluor 488 (Goat polyclonal) | Invitrogen | Cat#: A11029; RRID:AB_138404 |
Immunofluorescence (1:1000) |
| Antibody | Anti-Mouse Alexa Fluor 568 (Goat polyclonal) | Invitrogen | Cat# A11031; RRID:AB_144696 |
Immunofluorescence (1:1000) |
| Antibody | Anti-Mouse Alexa Fluor 647 (Goat polyclonal) | Invitrogen | Cat#: A21236; RRID:AB_2535805 |
Immunofluorescence (1:1000) |
| Antibody | Anti-Rabbit Alexa Fluor 568 (Goat polyclonal) | Invitrogen | Cat#: A11036; RRID:AB_10563566 |
Immunofluorescence (1:1000) |
| Antibody | Anti-Rabbit Alexa Fluor 405 (Goat polyclonal) | Invitrogen | Cat# A31556; RRID:AB_221605 |
Immunofluorescence (1:1000) |
| Antibody | Anti-Mouse IgG IRDye 680RD (Goat polyclonal) | Licor | Cat# 926-68070; RRID:AB_10956588 |
Western blot (1:20,000) |
| Antibody | Anti-Mouse IgG IRDye 800CW (Goat polyclonal) | Licor | Cat# 926-32210; RRID:AB_621842 |
Western blot (1:20,000) |
| Antibody | Anti-Rabbit IgG IRDye 680RD (Goat polyclonal) | Licor | Cat# 926-68071; RRID:AB_10956166 |
Western blot (1:20,000) |
| Antibody | Anti-Rabbit IgG IRDye 800CW (Goat polyclonal) | Licor | Cat# 926-32211; RRID:AB_621843 |
Western blot (1:20,000) |
| Recombinant DNA reagent | Plasmids used | This paper | N/A | Supplementary file 1 |
| Sequence-based reagent | HiLITR TEV-protease QPCR primers | This paper | N/A | Materials and methods: ‘Model selection’ |
| Sequence-based reagent | Random hexamer primer | Invitrogen | Cat# N8080127 | |
| Sequence-based reagent | Individual sgRNA sequences used | This paper | N/A | Supplementary file 1 |
| Sequence-based reagent | sgRNA libraries derived from hCRISPRi-v2 | Horlbeck et al., 2016 | RRID:Addgene_83969 | Supplementary file 2 |
| Peptide, recombinant protein | Fibronectin | Millipore | Cat# FC010 | |
| Peptide, recombinant protein | Bovine serum albumin | Fisher BioReagents | Cat# BP1600 | |
| Peptide, recombinant protein | Aprotinin | Sigma | Cat# A1153 | |
| Peptide, recombinant protein | Leupeptin | Roche | Cat# 11017101001 | |
| Peptide, recombinant protein | Endoproteinase LysC | Wako Laboratories | Cat# 12505061 | |
| Peptide, recombinant protein | Sequencing-grade trypsin | Promega | Cat# V5111 | |
| Commercial assay or kit | RNeasy Plus Mini Kit | Qiagen | Cat# 74134 | |
| Commercial assay or kit | QIAamp DNA Blood Maxi Kit | Qiagen | Cat# 51194 | |
| Commercial assay or kit | BCA Assay Kit | Pierce | Cat# 23225 | |
| Commercial assay or kit | MycoAlert Mycoplasma detection kit | Lonza | Cat# LT07-118 | |
| Chemical compound, drug | 1% penicillin-streptomycin | Corning | Cat# 30-002CI | |
| Chemical compound, drug | GlutaMAX | Gibco | Cat# 35050061 | |
| Chemical compound, drug | Puromycin | Sigma | Cat# P8833 | |
| Chemical compound, drug | Blasticidin | Corning | Cat# 30-100-RB | |
| Chemical compound, drug | Hygromycin | Corning | Cat# 30-240-CR | |
| Chemical compound, drug | Geneticin G418 | Thermo Fisher | Cat# 10131035 | |
| Chemical compound, drug | Polyethyleneimine (PEI) | Polysciences | Cat# 24765-1 | |
| Chemical compound, drug | Polybrene | Millipore | Cat# TR-1003-G | |
| Chemical compound, drug | Doxycycline | Sigma | Cat# C9891 | |
| Chemical compound, drug | MitoTracker Deep Red FM | Invitrogen | Cat# M22426 | |
| Chemical compound, drug | Paraformaldehyde | RICCA | Cat# 3180 | |
| Chemical compound, drug | Triton X-100 | Sigma | Cat# T9284 | |
| Chemical compound, drug | TMTpro isobaric mass tagging reagent | Thermo | Cat# A44520 | |
| Software, algorithm | CasTLE | Morgens et al., 2016 | https://bitbucket.org/dmorgens/castle/src | |
| Software, algorithm | Bowtie 2 | Langmead and Salzberg, 2012 | RRID::SCR_016368 | |
| Software, algorithm | SH800S Cell Sorter Software (versions 2.1.2, 2.1.5) | SONY | N/A | |
| Software, algorithm | Everest (version 2.3) | BioRad | N/A | |
| Software, algorithm | FlowJo (version 10.7.1) | FlowJo | N/A | |
| Software, algorithm | SlideBook 5.0 software | Intelligent Imaging Innovations | N/A | |
| Software, algorithm | StepOne Software (version 2.2.2) | Applied Biosystems | N/A | |
| Software, algorithm | Limma (version 3.42.2) | Smyth, 2004 | RRID:SCR_010943 | |
| Other | Fetal bovine serum | Avantor | Cat# 97068-085 | |
| Other | SuperScript III Reverse Transcriptase | Invitrogen | Cat# 18080093 | |
| Other | RiboLock RNAse inhibitor | Thermo Scientific | Cat# EO0382 | |
| Other | Maxima SYBR Green/ROX qPCR Master Mix | Thermo Scientific | Cat# K0221 | |
| Other | Herculase II Fusion | Agilent | Cat# 600679 | |
| Other | Protease Inhibitor Cocktail | Sigma | Cat# P8849 | |
| Other | Precision Plus Protein All Blue Prestained Standards | BioRad | Cat# 1610373 |