Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Homo sapiens) | RPL22 | NA | ENSEMBL:ENSG00000116251 | |
| Gene (H. sapiens) | RPL22L1 | NA | ENSEMBL:ENSG00000163584 | |
| Gene (H. sapiens) | MDM4 | NA | ENSEMBL:ENSG00000198625 | |
| Strain, strain background (Escherichia coli) | Endura ElectroCompetent Cells | Lucigen | Cat# 60242-2 | |
| Cell line (H. sapiens) | ‘MV4;11’ | ATCC | Cat# CRL-9591; RRID:CVCL_0064 | |
| Cell line (H. sapiens) | ‘MV4;11 NT’ | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | ‘MV4;11 RPL22 KO’ | This study | NA | See ’Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | ‘MV4;11 Cas9’ | This study | NA | See ‘Generation of Cas9-expressing MV4;11 cells’ |
| Cell line (H. sapiens) | MOLM13 | DMSZ | Cat# ACC554; RRID:CVCL_2119 | |
| Cell line (H. sapiens) | MOLM13 NT | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | MOLM13 RPL22 KO | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | K562 | ATCC | Cat# CCL-243; RRID:CVCL_0004 | |
| Cell line (H. sapiens) | K562 NT | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | K562 RPL22 KO | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | HEK293T | ATCC | Cat# CRL-11268; RRID:CVCL_1926 | |
| Antibody | Anti-p53 (DO-1) (mouse monoclonal) | Santa Cruz Biotechnology | Cat# sc-126; RRID:AB_628082 | (1:2000) |
| Antibody | Anti-RPL22 (52) (mouse monoclonal) | Santa Cruz Biotechnology | Cat# sc-136413; RRID:AB_10658965 | (1:1000) |
| Antibody | Anti-RPL22L1 (rabbit polyclonal) | Thermo Fisher Scientific | Cat# PA5-63266; RRID:AB_2646731 | (1:1000) |
| Antibody | Anti-MDMX (mouse monoclonal) | Sigma-Aldrich | Cat# M0445; RRID:AB_532256 | (1:1000) |
| Antibody | Anti-p21 Waf1/Cip1 (12D1) (rabbit monoclonal) | Cell Signaling Technology | Cat# 2947; RRID:AB_823586 | (1:1000) |
| Antibody | Anti-⍺-actinin (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 12413; RRID:AB_2797903 | (1:1000) |
| Antibody | Anti-GAPDH (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 8884; RRID:AB_11129865 | (1:2000) |
| Antibody | Anti-nucleophosmin (mouse monoclonal) | Abcam | Cat# ab10530; RRID:AB_297271 | (1:500) |
| Antibody | Anti-Phospho-Histone H2A.X (Ser139) (20E3) (rabbit monoclonal) | Cell Signaling Technology | Cat# 9718; RRID:AB_2118009 | (1:250) |
| Antibody | Goat anti-mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-11001; RRID:AB_2534069 | (1:500) |
| Antibody | Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | Cat# A-11037; RRID:AB_2534095 | (1:500) |
| Antibody | Anti-GAPDH (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 8884; RRID:AB_11129865 | (1:2000) |
| Antibody | Goat anti-mouse IgG, Light chain specific (HRP) | Jackson ImmunoResearch Laboratories, Inc | Cat# 115-035-174; RRID:AB_2338512 | (1:5000) |
| Antibody | Goat anti-rabbit IgG, HRP-linked antibody | Cell Signaling Technology | Cat# 7074; RRID:AB_2099233 | (1:5000) |
| Recombinant DNA reagent | lentiCas9-Blast | PMID:25075903 | Addgene plasmid# 52962; RRID:Addgene_52962 | |
| Recombinant DNA reagent | psPAX2 | Addgene | Addgene plasmid# 12260; RRID:Addgene_12260 | |
| Recombinant DNA reagent | pMD2.G | Addgene | Addgene plasmid# 12259; RRID:Addgene_12259 | |
| Recombinant DNA reagent | Human GeCKOv2 CRISPR Knockout Pooled Library (A+B) in lentiGuide-PURO |
PMID:25075903 | Addgene plasmid# 1000000048 | |
| Recombinant DNA reagent | lentiGuide-PURO | PMID:25075903 | Addgene plasmid# 52963; RRID:Addgene_52963 | |
| Commercial assay or kit | cOmplete, EDTA-free, Protease Inhibitor Cocktail | Roche | Cat# 11873580001 | |
| Commercial assay or kit | PhosSTOP | Roche | Cat# 4906837001 | |
| Commercial assay or kit | Pefabloc SC | Roche | Cat# 11429868001 | |
| Commercial assay or kit | TURBO DNase (2 U/µL) | Invitrogen | Cat# AM2238 | |
| Commercial assay or kit | RNase I, E. coli | Lucigen | Cat# N6901K | |
| Commercial assay or kit | SUPERaseIn RNase Inhibitor | Invitrogen | Cat# AM2694 | |
| Commercial assay or kit | TRIzol Reagent | Invitrogen | Cat# 15596018 | |
| Commercial assay or kit | SYBR Gold Nucleic Acid Gel Stain | Invitrogen | Cat# S11494 | |
| Commercial assay or kit | T4 Polynucleotide Kinase | New England BioLabs | Cat# M0201S | |
| Commercial assay or kit | T4 RNA Ligase 2, truncated K227Q | New England BioLabs | Cat# M0351S | |
| Commercial assay or kit | SuperScript III Reverse Transcriptase | Invitrogen | Cat# 18080085 | |
| Commercial assay or kit | Random Hexamers | Invitrogen | Cat# N8080127 | |
| Commercial assay or kit | CircLigase II ssDNA Ligase | Lucigen | Cat# CL9021K | |
| Commercial assay or kit | LD-Dithiothreitol | MilliporeSigma | Cat# D9779 | |
| Commercial assay or kit | Iodoacetamide | MilliporeSigma | Cat# I1149 | |
| Commercial assay or kit | o-Phosphoric acid, 85% | Fisher Scientific | Cat# A260-500 | |
| Commercial assay or kit | Water, Optima LC/MS Grade | Fisher Scientific | Cat# W6-4 | |
| Commercial assay or kit | Methanol, Optima LC/MS Grade | Fisher Scientific | Cat# A456 | |
| Commercial assay or kit | Triethylammonium bicarbonate buffer | MilliporeSigma | Cat# T7408 | |
| Commercial assay or kit | Trypsin Gold, Mass Spectrometry Grade | Promega | Cat# V5280 | |
| Commercial assay or kit | Formic Acid, LC/MS Grade | Thermo Scientific Pierce | Cat# 28905 | |
| Commercial assay or kit | Acetonitrile, Optima LC/MS Grade | Fisher Scientific | Cat# A955-1 | |
| Commercial assay or kit | Phusion High Fidelity DNA polymerase | New England BioLabs | Cat# M0530S | |
| Commercial assay or kit | BsmBIv2 | New England BioLabs | Cat# R0739S | |
| Commercial assay or kit | DNase I (RNase-free) | New England BioLabs | Cat# M0303S | |
| Commercial assay or kit | RNA Clean and Concentrator-25 | Zymo Research | Cat# R1017 | |
| Commercial assay or kit | RNasin Ribonuclease Inhibitor | Promega | Cat# N2515 | |
| Commercial assay or kit | SYBR Safe DNA Gel Stain | Invitrogen | Cat# S33102 | |
| Commercial assay or kit | Click-iT Cell Reaction Buffer Kit | Invitrogen | Cat# C10269 | |
| Commercial assay or kit | Neon Transfection System 10 µL Kit | Thermo Scientific | Cat# MPK1096 | |
| Commercial assay or kit | Gene Knockout Kit v2 – human – RPL22 | Synthego | NA | |
| Commercial assay or kit | Negative Control, Scrambled sgRNA#1, mod-sgRNA |
Synthego | NA | |
| Commercial assay or kit | ProLong Gold Antifade Mountant | Thermo Fisher Scientific | Cat# P36934 | |
| Commercial assay or kit | Lipofectamine 3000 Transfection Reagent | Invitrogen | Cat# L3000075 | |
| Commercial assay or kit | QuantiGene Plex panel | Thermo Fisher Scientific | NA | |
| Commercial assay or kit | QuantiGene Sample Processing Kit for cultured cells | Thermo Fisher Scientific | Cat# QS0100 | |
| Commercial assay or kit | QuantiGene Plex Assay kits | Thermo Fisher Scientific | Cat# QP1013 | |
| Commercial assay or kit | Pierce BCA Protein Assay Kit | Thermo Scientific | Cat# PI23225 | |
| Commercial assay or kit | Clarity Western ECL Substrate | Bio-Rad | Cat# 1705061 | |
| Commercial assay or kit | Qubit RNA High Sensitivity Assay Kit | Invitrogen | Cat# Q32852 | |
| Commercial assay or kit | Direct-zol RNA Miniprep | Zymo Research | Cat# R2050 | |
| Commercial assay or kit | RiboCop rRNA Depletion Kit V1.2 | Lexogen | Cat# 037.24 | |
| Commercial assay or kit | Quick-DNA MidiPrep Plus Kit | Zymo Research | Cat# D4075 | |
| Commercial assay or kit | NEBNext High Fidelity 2X PCR Master Mix |
New England BioLabs | Cat# M0541L | |
| Commercial assay or kit | Zymo-Spin V Columns with Reservoir | Zymo Research | Cat# C1016-25 | |
| Commercial assay or kit | NucleoSpin Gel and PCR Clean-up | Macherey-Nagel | Cat# 740609.250 | |
| Commercial assay or kit | Gibson Assembly Master Mix | New England BioLabs | Cat# E2611S | |
| Commercial assay or kit | NucleoBond Xtra Maxi EF | Macherey-Nagel | Cat# 740424.10 | |
| Commercial assay or kit | Q5 DNA Polymerase | New England BioLabs | Cat# M0491S | |
| Commercial assay or kit | Taq DNA Polymerase with Standard Taq Buffer |
New England BioLabs | Cat# M0273S | |
| Commercial assay or kit | SYBR Safe DNA Gel Stain | Invitrogen | Cat# S33102 | |
| Commercial assay or kit | KAPA SYBR Fast qPCR Master Mix (2×) |
Roche | Cat# 07959397001 | |
| Commercial assay or kit | CellTiter-Glo Luminescent Cell Viability Assay |
Promega | Cat# G7572 | |
| Chemical compound, drug | Blasticidin S Hydrochloride Powder | Research Products International | Cat# B12200-0.05 | |
| Chemical compound, drug | DMSO | Sigma | Cat# D2650 | |
| Chemical compound, drug | C6 | PMID:30865883 | N/A | |
| Chemical compound, drug | C16 | PMID:31858797 | N/A | |
| Chemical compound, drug | 2’-Azido-2’-deoxycytidine | Biosynth | Cat# NA05412 | |
| Chemical compound, drug | Actinomycin D | Cayman Chemical Company | Cat# 11421-10mg | |
| Chemical compound, drug | MB 680R DBCO | Vector Laboratories | Cat# CCT-1462 | |
| Chemical compound, drug | Cycloheximide | Research Products International | Cat# C81040-1.0 | |
| Chemical compound, drug | OPP (O-propargyl-puromycin) | Invitrogen | Cat# C10459 | |
| Chemical compound, drug | Hoechst 33342 | Thermo Fisher Scientific | Cat# H3570 | |
| Chemical compound, drug | Alexa Fluor 647 Azide, Triethylammonium Salt |
Invitrogen | Cat# A10277 | |
| Chemical compound, drug | Cycloheximide | Sigma | Cat# C4859-1ML | |
| Chemical compound, drug | Nutlin-3a | Cayman Chemical Company | Cat# 18585 | |
| Chemical compound, drug | Rapamycin | MedChem Express | Cat# HY-10219 | |
| Chemical compound, drug | Pinometostat | Cayman Chemical Company | Cat# 16175 | |
| Chemical compound, drug | Harmine | Sigma-Aldrich | Cat# 286044 | |
| Chemical compound, drug | Mivebresib | Cayman Chemical Company | Cat# 21033 | |
| Chemical compound, drug | Venetoclax | Cayman Chemical Company | Cat# 16233 | |
| Chemical compound, drug | Etoposide | Cayman Chemical Company | Cat# 12092 | |
| Chemical compound, drug | Olaparib | Cayman Chemical Company | Cat# 10621 | |
| Chemical compound, drug | VE-821 | Cayman Chemical Company | Cat# 17587 | |
| Chemical compound, drug | Pemrametostat | Selleck Chemicals | Cat# S8664 | |
| Chemical compound, drug | Alvespimycin | Cayman Chemical Company | Cat# 11036 | |
| Software, algorithm | R | The R Foundation | RRID:SCR_001905 | https://www.r-project.org |
| Software, algorithm | drc | Ritz et al., 2015; Ritz and Streibig, 2021 | NA | https://github.com/DoseResponse/drc |
| Software, algorithm | CHOPCHOP | Labun et al., 2019 | RRID:SCR_015723 | https://chopchop.cbu.uib.no |
| Software, algorithm | count_spacers.py | Joung et al., 2017; Joung, 2017 | NA | https://github.com/fengzhanglab/Screening_Protocols_manuscript/blob/master/design_targeted_library.py |
| Software, algorithm | SynergyFinder Plus | Zheng et al., 2022 | RRID:SCR_019318 | https://synergyfinder.org/ |
| Software, algorithm | PASWR | Ugarte et al., 2015; Arnholt, 2022 | NA | https://github.com/cran/PASWR |
| Software, algorithm | cutadapt | Martin, 2011 | RRID:SCR_011841 | https://github.com/marcelm/cutadapt/ |
| Software, algorithm | sabre | NA | RRID:SCR_011843 | https://github.com/najoshi/sabre |
| Software, algorithm | bowtie2 | Langmead and Salzberg, 2012 | RRID:SCR_016368 | https://github.com/BenLangmead/bowtie2 |
| Software, algorithm | STAR | Dobin et al., 2013 | RRID:SCR_004463 | https://github.com/alexdobin/STAR |
| Software, algorithm | UMI-tools | Smith et al., 2017 | RRID:SCR_017048 | https://github.com/CGATOxford/UMI-tools |
| Software, algorithm | BEDTools | Quinlan and Hall, 2010 | RRID:SCR_006646 | https://github.com/arq5x/bedtools2 |
| Software, algorithm | Xtail | Xiao et al., 2016; xryanglab, 2016 | NA | https://github.com/xryanglab/xtail |
| Software, algorithm | riboWaltz | Lauria et al., 2018 | RRID:SCR_016948 | https://github.com/LabTranslationalArchitectomics/riboWaltz |
| Software, algorithm | featureCounts | Liao et al., 2014 | RRID:SCR_012919 | http://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| Software, algorithm | DESeq2 | Love et al., 2014 | RRID:SCR_015687 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Software, algorithm | MAGeCK | Li et al., 2014; Li and Song, 2022 | NA | https://sourceforge.net/p/mageck/wiki/Home/ |
| Software, algorithm | Maxquant | Cox and Mann, 2008 | RRID:SCR_014485 | https://cox-labs.github.io/coxdocs/maxquant_instructions.html |
| Software, algorithm | Andromeda | Cox et al., 2011 | NA | https://cox-labs.github.io/coxdocs/andromeda_instructions.html |
| Software, algorithm | Msstats | Choi et al., 2014 | RRID:SCR_014353 | https://msstats.org/ |
| Software, algorithm | fgsea | Korotkevich et al., 2021 | RRID:SCR_020938 | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| Software, algorithm | Biorender | NA | RRID:SCR_018361 | https://biorender.com |
| Software, algorithm | PyMOL | NA | RRID:SCR_000305 | https://pymol.org/2/ |
| Software, algorithm | rMATS | Shen et al., 2014 | RRID:SCR_013049 | https://rnaseq-mats.sourceforge.net |
| Software, algorithm | Molecular Signatures Database | Liberzon et al., 2011 | RRID:SCR_016863 | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp |
| Software, algorithm | Universal Protein Resource | Bateman et al., 2021 | RRID:SCR_002380 | https://www.uniprot.org |
| Software, algorithm | FlowJo | NA | RRID:SRC_008520 | https://www.flowjo.com/solutions/flowjo |
| Software, algorithm | Empiria Studio | LI-COR | RRID:SCR_022512 | https://www.licor.com/bio/empiria-studio/ |
| Software, algorithm | NIS-Elements AR 5.42.03 64-bit | Nikon Instruments | RRID:SCR_014329 | https://www.nikoninstruments.com/Products/Software |
| Software, algorithm | Fiji | Fiji/ImageJ | RRID:SCR_002285 | http://fiji.sc |
| Other | S-Trap Micro Columns | ProtiFi | Cat# C02-micro-80 | |
| Other | Jupiter 3 um C18 300A, Bulk packaging | Phenomenex | Cat# 04A-4263 | |
| Other | Molex Polymicro Capillary 100 um × 363 um |
Fisher Scientific | Cat# 50-110-8623 | |
| Other | Neon Transfection System | Thermo Fisher Scientific | Cat# MPK5000 | |
| Other | Luminex FLEXMAP 3D System | Invitrogen | Cat# APX1342 | |
| Other | 4–20% Mini-PROTEAN TGX Precast Gel |
Bio-Rad | Cat# 4561096 | |
| Other | Amersham Protran Western Blotting Membranes, Nitrocellulose | Cytiva | Cat# GE10600001 | |
| Other | C1000 Touch Thermal Cycler Chassis | Bio-Rad | Cat# 1841100 | |
| Other | CFX96 Optical Reaction Module for Real-Time PCR System |
Bio-Rad | Cat# 1845097 | |
| Other | ChemiDoc Imaging System | Bio-Rad | Cat# 17001401 | |
| Other | Thick-wall Polycarbonate Tubes, 13 × 51 mm |
Beckman-Coulter | Cat# 349622 | |
| Other | Novex TBE-Urea Gels 15%, 12 well | Invitrogen | Cat# EC68852BOX | |
| Other | Costar Spin-X Centrifuge Tube Filters | Corning | Cat# CLS8162 | |
| Other | Novex TBE Gels, 8%, 15 well | Invitrogen | Cat# EC62155BOX | |
| Other | GloMax Explorer Multimode Microplate Reader | Promega | Cat# GM3500 | |
| Other | Orbitrap Exploris 480 Mass Spectrometer | Thermo Scientific | Cat# BRE725533 |