KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-β-Actin, HRP-linked | Sigma-Aldrich | Cat# A3854-200UL |
| Mouse monoclonal anti-FLAG | Sigma-Aldrich | Cat# F1804 |
| Rabbit polyclonal anti-H3K4me3 | Sigma-Aldrich | Cat# 07–473 |
| Rat monoclonal anti-HA (clone 3F10), HRP-linked | Roche | Cat# 12013819001 |
| Rabbit monoclonal anti-SCP4 | Cell Signaling Technology | Cat# 6932 |
| Rabbit polyclonal anti-mouse IgG, HRP-linked | Agilent/Dako | Cat# P026002-2 |
| Donkey anti-rabbit IgG, HRP-linked | Cytiva/Amersham | Cat# NA934 |
| Bacterial and virus strains | ||
| MegaX DH10B T1R Electrocomp Cells | Invitrogen | Cat# C640003 |
| Chemicals, peptides, and recombinant proteins | ||
| 2-Mercaptoethanol | Sigma-Aldrich | Cat# M6250 |
| 2x Laemmli Sample Buffer | BIO-RAD | Cat# 1610737 |
| Agarose, Standard, Low Electroendosmosis (EEO) | Avantor | Cat# A426-07 |
| Anti-FLAG ® M2 Affinity Gel | Sigma-Aldrich | Cat# A2220-10ML |
| Blasticidin S HCl | Thermo Fisher Scientific | Cat# A1113903 |
| Blasticidin S HCl | Thermo Fisher Scientific | Cat# A1113903 |
| BsmBI | New England BioLabs | Cat# R0739 |
| Cell Lysis Buffer | Cell Signaling Technology | Cat# 9803 |
| Chloroform | Sigma-Aldrich | Cat# 288306 |
| D-Luciferin | Goldbio | Cat# 115144-35-9 |
| Dimethyl Sulfoxide | Sigma-Aldrich | Cat# D2650 |
| DMEM with 4.5 g/L glucose, L-glutamine & sodium pyruvate | Cellgro | Cat# 10–013-CV |
| DNA Polymerase I, Large (Klenow) Fragment | New England Biolabs | Cat# M0210L |
| EZview™ Red Anti-HA Affinity Gel | Sigma-Aldrich | Cat# E6779-1ML |
| Geneticin Selective Antibiotic (G-418 Sulfate) | Thermo Fisher Scientific | Cat# 10131035 |
| Geneticin Selective Antibiotic (G418 Sulfate) | Thermo Fisher Scientific | Cat# 10131035 |
| HEPES | Life Technologies | Cat# 15630-130 |
| ImmPACT DAB peroxidase (HRP) substrate | Vector | Cat# SK-4105 |
| Isopropanol | Sigma-Aldrich | Cat# 190674 |
| Klenow Fragment (3′-5′ exo-) | New England Biolabs | Cat# M0212L |
| Opti-MEM® | Thermo Fisher Scientific | Cat# 31985062 |
| Penicillin/Streptomycin | Thermo Fisher Scientific | Cat# 15140122 |
| Phusion Flash High-Fidelity PCR Master Mix | Thermo Fisher Scientific | Cat# F548S |
| Phusion® Hot Start Flex DNA Polymerase | New England Biolabs | Cat# M0535 |
| Pierce™ Anti-HA Magnetic Beads | Thermo Fisher Scientific | Cat# 88837 |
| Polybrene | EMD Millipore | Cat# TR-1003-G |
| Polyethylenimine, Linear, MW 25,000 (PEI 25000) | Polysciences | Cat# 23966-1 |
| Puromycin dihydrochloride | Sigma-Aldrich | Cat# P8833 |
| RPMI 1640 w/ L-glutamine | Fisher Scientific | Cat# MT10040CV |
| T4 DNA polymerase | New England Biolabs | Cat# M0203L |
| T4 polynucleotide kinase | New England Biolabs | Cat# M0201L |
| TRIzol Reagent | Thermo Fisher Scientific | Cat# 15596018 |
| Critical commercial assays | ||
| Agilent High Sensitivity DNA Kit | Agilent Genomics | Cat# 5067-4626 |
| FITC Annexin V Apoptosis Detection Kit | BD Biosciences | Cat# 556547 |
| FITC BrdU Flow Kit | BD Biosciences | Cat# 559619 |
| Gibson Assembly Master Mix | New England Biolabs | Cat# E2611 |
| In-Fusion HD Cloning Kit | Takara Bio | Cat# 638909 |
| MiniElute PCR Purification Kit | QIAGEN | Cat# 28004 |
| MiSeq Reagent Kit V3 150-cycle | Illumina | Cat# MS-102-3001 |
| Pierce™ BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23225 |
| Power SYBR Green Master Mix | Thermo Fisher Scientific | Cat# 4368577 |
| QIAamp DNA Mini Kit | QIAGEN | Cat# 51304 |
| QIAquick Gel Extraction Kit | QIAGEN | Cat# 28704 |
| Quick Ligation Kit | New England Biolabs | Cat# M2200L |
| TruSeq RNA Sample Prep Kit v2 | Illumina | Cat# RS-122-2001 |
| Deposited data | ||
| RNA-Seq | This study | GEO: GSE174169 |
| RNA-Seq | Tarumoto et al. (2018) | GEO: GSE109491 |
| RNA-Seq | Xu etal. (2018) | GEO: GSE104308 |
| Human reference genome GRCh37/hg19 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/grc/human |
| Human reference genome GRCh37/hg38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/grc/human |
| Raw Mass Spectrometry Data Files | This study | ProteomeXchange Consortium with the dataset identifier PXD029769. Additional identifiers https://doi.org/10.25345/C5786Q, MassIVE (MSV000088383) |
| Raw Metabolomics Data Files | This study | MetaboLights database with identifier MTBLS3707 |
| Experimental models: Cell lines | ||
| Human: A549 | ATCC | CCL-185 |
| Human: AsPC-1 | ATCC | CRL-1682 |
| Human: HEK293T | ATCC | CRL-3216 |
| Human: HEL | ATCC | TIB-180 |
| Human: K562 | ATCC | CCL-243 |
| Human: Kasumi-1/Cas9 | Robert Roeder | N/A |
| Human: MA9-ITD | Wunderlich et al. (2013) | N/A |
| Human: MA9-RAS | Wunderlich et al. (2013) | N/A |
| Human: MIAPaCa-2 | ATCC | CRL-142 |
| Human: ML-2 | DSMZ | ACC 15 |
| Human: MOLM-13 | DSMZ | ACC 554 |
| Human: MV4-11 | ATCC | CRL-9591 |
| Human: NCI-H1048 [H1048] | ATCC | CRL-5853 |
| Human: NOMO-1 | DSMZ | ACC 542 |
| Human: OCI-AML3 | DSMZ | ACC 582 |
| Human: PANC-1 | ATCC | CRL-1469 |
| Human: RD | ATCC | CCL-136 |
| Human: RH30 | DSMZ | ACC 489 |
| Human: RH4 | NA | RRID: CVCL_5916 |
| Human: SEM | DSMZ | ACC 546. |
| Human: SET-2 | DSMZ | ACC 608 |
| Human: SUIT-2 | JCRB | JCRB1094 |
| Human: THP-1 | ATCC | TIB-202 |
| Human: U937 | ATCC | CRL-1593.2 |
| Mouse: NIH3T3 | ATCC | CRL-1658 |
| Mouse: RN2 | Zuber etal. (2011) | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: NSG | The Jackson Laboratory | Stock No: 005557 |
| Oligonucleotides | ||
| sgRNA sequences, see Tables S3 and S4 | This study | N/A |
| Primers, see Tables S3 and S4 | This study | N/A |
| Recombinant DNA | ||
| LRG (Lenti_sgRNA_EFS_GFP) | Shi etal. (2015) | Addgene plasmid # 65656 |
| LRG2.1 | Tarumoto et al. (2018) | Addgene plasmid # 108098 |
| LRCherry2.1 | Tarumoto et al. (2018) | N/A |
| LRG2.1-Blast | Klingbeil, unpublished | N/A |
| LentiV_Cas9_puro | Tarumoto et al. (2018) | Addgene plasmid # 108100 |
| LentiV_Neo | Tarumoto et al. (2018) | N/A |
| Lenti-luciferase-P2A-Neo | Wei etal. (2021) | Addgene plasmid # 105621 |
| psPAX2 | N/A | Addgene plasmid # 12260 |
| CTDSPL2 cDNA | Horizon Discovery | Clone ID: 5744745 |
| partial STK35 cDNA | Horizon Discovery | Clone ID: 9021751 |
| PDIK1L cDNA | Horizon Discovery | Clone ID: 4828997 |
| Software and algorithms | ||
| Aminode | Chang et al. (2018) | http://www.aminode.org/ |
| CSHL sgRNA Design Tool | El Demerdash, unpublished | https://mojica.cshl.edu |
| DESeq2 | Love et al. (2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| FlowJo | TreeStar Inc. | https://www.flowjo.com |
| GraphPad Prism v.5 and v.9 | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| HTSeq-Count v.0.6.1p1 | Anders et al. (2015) | https://htseq.readthedocs.io/en/master/ |
| HUGO Gene Nomenclature Committee (HGNC) | N/A | https://www.genenames.org |
| IUPred2A | Meszaros et al. (2018) | https://iupred2a.elte.hu |
| Kallisto | Bray et al. (2016) | https://pachterlab.github.io/kallisto/ |
| Metascape | Tripathi et al. (2015) | http://metascape.org |
| Salmon v.1.0 | Patro et al. (2017) | https://salmon-tddft.jp/wiki/Download-v.1.0.0 |
| STAR v.2.5.2b-1 | Dobin et al. (2013) | https://github.com/alexdobin/STAR |
| UCSC Genome Browser | UCSC | http://genome.ucsc.edu |