| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-DNMT3A (64B1446) | Novus Biologicals™ | NB120-13888; RRID: AB_1149786 |
| Rabbit polyclonal anti-MEF2B | ThermoFisher Scientific | PA5101143; RRID: AB_2850587 |
| Rabbit monoclonal anti-beta-Actin | Cell signaling | 4967S; RRID: AB_330288 |
| GAPDH-HRP | CST | 3683; RRID: AB_1642205 |
| Anti-rabbit IgG, HRP-linked Antibody | Cell signaling | 7074; RRID: AB_2099233 |
| Anti-mouse IgG, HRP-linked Antibody | Cell signaling | 7076; RRID: AB_330924 |
| Mouse monoclonal anti-FLAG® M2 antibody | Sigma-Aldrich | F1804; RRID: AB_262044 |
| APC mouse anti-human CD38 | BD biosciences | 555462; RRID: AB_398599 |
| PE mouse anti-human CD19 Clone 4G7 | R&D biotechne | MAB4867R |
| anti human CD20 FITC-LT20 clone, mouse IgG1k | Miltenyi Biotec | 130-113-373; RRID: AB_2726142 |
| 5mC antibody | epigentek | A-1014-050 |
| Mouse monoclonal [9E10] to Myc tag | abcam | ab32; RRID: AB_303599 |
| Rabbit monoclonal- MYC antibody (Y69) | abcam | ab32072; RRID: AB_731658 |
| Bacteria and virus strains | ||
| DH5α | Invitrogen™ | 18265017 |
| Biological samples | ||
| B cells from cord blood | Stem Cell Technologies | 70013 |
| Primary MCL cells | Mohanty et al.57 | https://doi.org/10.1182/blood-2018-05-851667 |
| Chemicals, peptides, and recombinant proteins | ||
| Ibrutinib | Selkchem | S2680 |
| IM156 | Targetmol | S9604 |
| Decitabine | Targetmol | T1508-SB100 |
| JC-1 Dye | Invitrogen™ | T3168 |
| MitoSOX™ Red Mitochondrial Superoxide Indicator | Thermo Fisher Scientific | M36008 |
| MitoTracker™ Deep Red | Thermo Fisher Scientific | M22426 |
| SuperSignal™ West Femto Maximum Sensitivity Substrate | Thermo Fisher Scientific | 34096 |
| Pierce™ BCA Protein Assay Kit | Thermo Fisher Scientific | 23225 |
| Trizol for RNA extraction | Thermo Fisher Scientific | 15596018 |
| APC Annexin V | BD pharmingen | 550474 |
| PI flow dye (BD) | BD pharmingen | 556463 |
| Doxycycline hyclate | Sigma-Aldrich | D9891 |
| RPMI-1640 medium (1x) -L-glutamine | hyclone | SH30096.LS |
| DMEM/High glucose with L-glutamine, sodium pyruvate | hyclone | SH30243.FS |
| FBS | R&D | S10350 |
| XF RPMI Medium ph7.4 | Agilent | 103576 |
| XF Calibrant, ph 7.4 | Agilent | 100840 |
| Corning® Cell-Tak™ Cell and Tissue Adhesive | Corning | 354240 |
| pen/strep solution | lonza | 17-602E |
| Corning® glutagro™ | Corning | 25-015-CI |
| MEM Non-Essential Amino Acid Solution (100X) | Lonza | 13-114E |
| Sodium Pyruvate Solution | GE Healthcare Life Sciences | SH30239.01 |
| Trypan Blue Solution (w/v) in PBS | corning | 25-900-CI |
| Protease inhibitor cocktail | sigma-aldrich | P8340 |
| PMSF Protease Inhibitor | Thermo Scientific™ | 36978 |
| D-Luciferin, Sodium Salt | Gold Biotechnology | LUCNA |
| Triton X-100 | EMD MILLIPORE | 94101L |
| pierce 16% formaldehyde (w/v), methanol-free | pierce | 28908 |
| PureLink™ RNase A | Invitrogen | 12091021 |
| Critical commercial assays | ||
| Galacto-Star™ β-Galactosidase Reporter Gene Assay System | Thermo Fisher Scientific | T1012 |
| SuperScript™ IV First-Strand Synthesis System | Thermo Fisher Scientific | 18091050 |
| GeneArt® Site-Directed Mutagenesis System | invitrogen | A13282 |
| Maxwell RSC Culture Cells DNA kit | Promega | AS1620 |
| Luciferase Assay System | Promega | E1500 |
| CellTiter-Glo(R) 2.0 Assay | Promega | G9242 |
| APC BrDu flow kit | BD pharmingen | 552598 |
| Seahorse XF Cell Mito Stress Test Kit | Agilent | 103015 |
| QIAquick PCR Purification kit | QIAGEN | 28106 |
| SensiFast SYBR Hi-Rox Kit | Bioline | BIO-92005 |
| TruSeq Stranded mRNA Library Preparation Kit Set B | illumina | RS-122-2102 |
| TruSeq DNA LT Sample Prep Kit | Illumina | FC-121-2001 |
| Ovation Ultralow System V2 | NuGEN | 0344NB |
| Qbit dsDNA Broad range assay | Invitrogen | Q32850 |
| Deposited data | ||
| MCL-4 | This paper | PRJNA1077921 |
| MCL-5 | This paper | PRJNA1077921 |
| MCL-7 | This paper | PRJNA1077921 |
| MCL-9 | This paper | PRJNA1077921 |
| DNMT3A ChIP-seq in Z138 WT | This paper | GSE227976 |
| DNMT3A ChIP-seq in Z138#7 KO | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-uninduced-1 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-uninduced-2 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-uninduced-3 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-5 days-1 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-5 days-2 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-5 days-3 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-7 days-1 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-7 days-2 | This paper | GSE227976 |
| DNMT3A-Z138sgDNMT3A#7-dox-7 days-3 | This paper | GSE227977 |
| MEF2B ChIP-seq in GM12878 | Luo et al.89 | GSE127481 |
| H3K27ac in Z138 | Ryan et al.90 | GSE97541 |
| Experimental models: Cell lines | ||
| JeKo-1∗ | Li et al.6 | https://doi.org/10.1038/onc.2016.155 |
| Rec-1∗ | Li et al.6 | https://doi.org/10.1038/onc.2016.155 |
| Z138∗ | Li et al.6 | https://doi.org/10.1038/onc.2016.155 |
| Rec-1∗ | Li et al.6 | https://doi.org/10.1038/onc.2016.155 |
| Mino∗ | Li et al.6 | https://doi.org/10.1038/onc.2016.155 |
| JVM-13 | Zhang et al.13 | https://doi.org/10.1126/scitranslmed.aau1167 |
| Granta-519 | Zhang et al.13 | https://doi.org/10.1126/scitranslmed.aau1167 |
| Maver-1 | Zhang et al.13 | https://doi.org/10.1126/scitranslmed.aau1167 |
| JeKo-1 Ibrutinib resistant | Liu et al.75 | https://doi.org/10.1182/blood.2022018674 |
| Rec-1 Ibrutinib resistant | Liu et al.75 | https://doi.org/10.1182/blood.2022018674 |
| Experimental models: Mouse | ||
| NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | Jackson Laboratory | 5557 |
| Oligonucleotides | ||
| See Table S2 for sequences of oligonucleotides | N/A | |
| Recombinant DNA | ||
| pRSGT16-U6Tet-sg-HTS6C-CMV-TetRep-2A-TagRFP-2A-Puro | Cellecta | #SVCRU6T16-L |
| pR-CMV-Cas9–2A-Hygro | Cellecta | #SVC9-PS |
| phCMV-GalV-MTR | Caeser et al.91 | Addgene #163612 |
| pCDH-DNMT3A WT | This paper | N/A |
| pCDH-DNMT3A V716G | This paper | N/A |
| pCDNA.3-Myc-DNMT3A WT | Chen et al.92 | Addgene plasmid #35521 |
| pCDNA.3-Myc-DNMT3A D333A | This paper | N/A |
| pCDNA.3-Myc-DNMT3A V716G | This paper | N/A |
| pCDNA.3-Myc-DNMT1 | Li et al.93 | Addgene plasmid #36939 |
| pCDNA.3-Myc-DNMT3B1 | Chen et al.92 | Addgene plasmid #35522 |
| pGL3-tfam | This paper | N/A |
| Software and algorithms | ||
| ImageJ 142 software | NIH | https://imagej.nih.gov/ij/index.html |
| GraphPad Prism 9.0 | Graphpad | www.graphpad.com |
| FlowJo Software vX 10.0.7v2 | FLOWJO, LLC | https://www.flowjo.com/ |
| StringTie | Pertea et al.94 | https://ccb.jhu.edu/software/stringtie/ |
| DEseq2 | Love et al.95 | http://bioconductor.org/packages/DESeq2/ |
| Genrich | Gaspar96 | https://github.com/jsh58/Genrich |
| HISAT2 | Kim et al.97 | http://daehwankimlab.github.io/hisat2/ |
| ChIPSeeker | Wang et al.98 Yu et al.99 |
http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| deepTools-Correct GC bias | Benjamini et al.100 | https://deeptools.readthedocs.io/en/latest/ |
| GSEA v3.0 | Broad Institute | https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page |
| BioRender BioRender | BioRender | https://biorender.com/ |
| Igtegrative Gomomic Viewer v2.13.2 | Broad Institute | https://software.broadinstitute.org/software/igv/ |
| Custom Python script for manual correction of tumor segmentation | Pachitariu et al.,101 Stringer et al.102 | https://www.github.com/mouseland/cellpose |
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