| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-MEF2D | Abcam | Product #: ab32845 |
| Rabbit polyclonal anti-MEF2D | Bethyl Laboratories | Product #: A303-522A |
| Rabbit monoclonal anti-IRF8 | Abcam | Product #ab207418, Lot #GR3271578-1 |
| Rabbit polyclonal anti-PU.1 | Cell Signaling Technology | Product #: 2266 |
| Monoclonal ANTI-FLAG® M2 antibody | Sigma-Aldrich | Cat# F1804; RRID: AB_262044 |
| Mouse monoclonal anti-HA (clone 12CA5) | Laboratory of Gerd Blobel | N/A |
| Rabbit monoclonal anti-GAPDH | Cell Signalling Technology | Product #14C10 |
| Rabbit polyclonal anti-FKBP12 antibody | Abcam | Cat# ab24373 |
| Mouse monoclonal anti-VINCULIN | Santa Cruz Biotechnology | Product #: sc-73614 |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat# ab4729; RRID: AB_211829 |
| Rabbit polyclonal anti-H3K4me1 | Abcam | Product #: ab8895 |
| PerCP anti-mouse CD45 Antibody | Biolegend | Cat# 103130 |
| IgG from rabbit serum | Sigma-Aldrich | Cat#: I8140 |
| Alexa Fluor® 680 Goat anti-mouse IgG (H + L) | Life Technologies | Product #A21058, Lot #1692967 |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody | LI-COR | Product #926-3221, Lot #C81210-05 |
| Chemicals, peptides, and recombinant proteins | ||
| Halt Protease & Phosphatase Inhibitor Cocktail, EDTA-free (100x) | Thermo Fisher Scientific | Ref #78441, Lot #UF284419 |
| Glycogen | Roche | Ref #10901393001, Lot #11651224 |
| SuperScript II Reverse Transcriptase | Thermo Fisher Scientific | Cat# 18064014 |
| AMPure XP | Beckman Coulter | A63880 |
| Penicillin/Streptomycin | Thermo Fisher Scientific | 15140122 |
| Proteinase K | New England Biolabs | P8107S |
| Puromycin dihydrochloride | Sigma-Aldrich | P8833 |
| Blasticidin | Invitrogen | R21001 |
| Geneticin Selective Antibiotic (G418 Sulfate) | Thermo Fisher Scientific | 10131035 |
| Polyethylenimine, PEI | Polysciences, INC | 23966 |
| OPTI-MEM | Thermo Fisher Scientific | 31985070 |
| Hexadimethrine Bromide, Polybrene | Sigma-Aldrich | H9268 |
| Dynabeads Protein A | Thermo Fisher Scientific | Ref #10002D, Lot #00651865 |
| TRIzol Reagent | Thermo Fisher Scientific | 15596018 |
| T4 DNA polymerase | New England Biolabs | M0203L |
| T4 polynucleotide kinase | New England Biolabs | M0201L |
| Agarose, Standard, Low Electroendosmosis (EEO) | Avantor | A426-07 |
| 2-Mercaptoethanol | Sigma-Aldrich | M6250 |
| 30% Acrylamide/Bis Solution, 37.5:1 | Bio-Rad | 1610158 |
| 2XLaemmli Sample Buffer | Bio-Rad | 1610737 |
| Dimethyl Sulfoxide | Sigma-Aldrich | D2650 |
| Concanavalin A–coated Magnetic Beads | Bangs Laboratories | BP531 |
| Digitonin | EMD Millipore | 300410 |
| Spermidine | Sigma-Aldrich | S2501 |
| dTAG-47 | This study | N/A |
| pA-MN | This study | N/A |
| Spike-in DNA | Laboratory of Steven Henikoff | N/A |
| Roche Complete Protease Inhibitor (EDTA-free) tablets | Sigma-Aldrich | 5056489001 |
| DNA Polymerase I, Large (Klenow) Fragment | New England Biolabs | M0210 |
| Formaldehyde 37% Solution | Avantor | 2106-01 |
| RNase A | Thermo Fisher Scientific | EN0531 |
| Phenol/Chloroform/Isoamyl Alcohol | Thermo Fisher Scientific | BP1752I400 |
| NP-40 (Igepal CA-630) | Sigma | I8896 |
| rmIL3 | Peprotech | 213-13 |
| rmIL6 | Peprotech | 216-16 |
| rmSCF | Peprotech | 250-03 |
| Methylcellulose-based Medium with Recombinant for Mouse | STEMCELL technologies | M3434 |
| Critical commercial assays | ||
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | G7570 |
| In-Fusion HD Cloning Kit | Takara Bio | 638909 |
| 2x Phusion Master Mix | Thermo Scientific | F-548 |
| Direct-zol RNA Miniprep Plus | Zymo Research | R2072 |
| QuantSeq 3′ mRNA-seq Library Prep Kit for Illumina | Lexogen | 015.96 |
| Dead Cell Removal Kit | Miltenyi Biotec | 130-090-101 |
| Agilent High Sensitivity DNA Kit | Agilent | 5067-4626 |
| QIAquick PCR Purification Kit | QIAGEN | 28104 |
| Quick-DNA Miniprep Kit | ZYMO Research | D3025 |
| NucleoSpin Gel and PCR Clean-up Mini Kit | Macherey-Nagel | 740609.250 |
| Aligent RNA 6000 Nano Kit | Aligent | 5067-1511 |
| NEBNext® Library Quant Kit for Illumina | NEB | E7630 |
| NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® | NEB | E7770 |
| NEBNext® Poly(A) mRNA Magnetic Isolation Module | NEB | E7490 |
| Deposited data | ||
| RNA-seq, ChIP-seq and CUT&RUN data | This study | GSE186132 |
| ChIP-seq | (Tarumoto et al., 2018) | GSE109493 |
| ChIP-seq | (Mohaghegh et al., 2019) | GSE123872 |
| ChIP-seq | (Poppe et al., 2017) | GSE89212 |
| ChIP-seq and CUT&RUN | (Krivtsov et al., 2019) | GSE127508 |
| ChIP-seq | (Rathert et al., 2015) | GSE63782 |
| RNA-seq and ATAC-seq | (Corces et al., 2016) | GSE75384 |
| RNA-seq | (Cao et al., 2021) | GSE157249 |
| ChIP-seq and CUT&RUN | (Cao et al., 2021) | GSE157636 |
| ChIP-seq | (Minderjahn et al., 2020) | GSE128834 |
| RNA-seq | (Secker et al., 2020) | GSE148714 |
| RNA-seq | (Barabé et al., 2017) | GSE71800 |
| Dnase I-seq | (Assi et al., 2019) | GSE108316 |
| Experimental models: Cell lines | ||
| Human: MOLM-13 | DSMZ | ACC-554 |
| Human: MV4-11 | ATCC | CRL-9591 |
| Human: THP1 | ATCC | TIB-202 |
| Human: HEL | ATCC | TIB-180 |
| Human: OCI-AML3 | DSMZ | ACC-582 |
| Human: U937 | ATCC | CRL-1593.2 |
| Human: K562 | ATCC | CCL-243 |
| Human: JURKAT | ATCC | TIB-152 |
| Human: REH | ATCC | CRL-8286 |
| Human: HEK293T | ATCC | CRL-3216 |
| Human: A549 | ATCC | CCL-185 |
| Human : HUH7 | JCRB | JCRB0403 |
| Human: A375 | ATCC | CRL-1619 |
| Human: OCI-AML5 | Laboratory of James D. Griffin | NA |
| Human: MA9-ITD | (Wei et al., 2008; Wunderlich et al., 2013) | NA |
| Human: MA9-RAS | (Wei et al., 2008; Wunderlich et al., 2013) | NA |
| Experimental models: Organisms/strains | ||
| Constitutive-Cas9-GFP | JAX | Stock No: 026179 |
| Oligonucleotides | ||
| sgRNA sequence see Table S2 | This study | N/A |
| qPCR primers see Table S3 | This study | N/A |
| Recombinant DNA | ||
| LentiV_neo_empty | (Tarumoto et al., 2018) | Addgene: 108101 |
| LentiV_neo_SFFV_MEF2D_short | This study | N/A |
| LentiV_neo_SFFV_MEF2D_long | This study | N/A |
| LentiV_neo_IRF8 | (Cao et al., 2021) | N/A |
| LentiV_Cas9_puro | (Tarumoto et al., 2018) | N/A |
| LRG(Lenti_sgRNA_EFS_GFP) | (Tarumoto et al., 2018) | Addgene:65656 |
| LRG2.1 | (Tarumoto et al., 2018) | Addgene:108098 |
| LRcherry2.1 | (Tarumoto et al., 2018) | Addgene:108099 |
| pSL21-mCherry | (Chen et al., 2021) | Addgene:164410 |
| pRG212 | (Gier et al., 2020) | Addgene: 149722 |
| Software and algorithms | ||
| Bowtie2 v2.3.5 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| BEDtools v2.28.0 | (Quinlan and Hall, 2010) | http://bedtools.readthedocs.io/en/latest/ |
| Samtools v1.1 | (Li et al., 2009) | http://samtools.sourceforge.net |
| HOMER v4 | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ |
| bcl2fastq Conversion Software, v2.17 | Illumina, Inc. | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html |
| MACS2 v2.1 | (Zhang et al., 2008) | https://github.com/taoliu/MACS |
| UCSC Genome Browser | UCSC | http://genome.ucsc.edu/ |
| deepTools | (Ramírez et al., 2016) | https://deeptools.readthedocs.io/en/develop/ |
| Picard tools v1.96 | Broad Institute | https://github.com/broadinstitute/picard |
| STAR v2.5.2 | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| HTSeq, htseq-count, v0.6.1pL | (Anders et al., 2015) | https://htseq.readthedocs.io/en/release_0.11.1/ |
| R Bioconductor DESeq2 package v1.14.1 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| MSigDB v6.1 | (Liberzon et al., 2015) | http://software.broadinstitute.org/gsea/msigdb/index.jsp |
| Cufflinks | (Trapnell et al., 2013) | http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/ |
| deepTools | (Ramírez et al., 2016) | https://deeptools.readthedocs.io/en/develop/index.html |
| IGVtools, 2.4.10 | Broad Institute | https://software.broadinstitute.org/software/igv/igvtools |
| GraphPad Prism 7 | GraphPad Software | N/A |
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