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. Author manuscript; available in PMC: 2023 Mar 3.
Published in final edited form as: Mol Cell. 2022 Feb 18;82(5):1003–1020.e15. doi: 10.1016/j.molcel.2022.01.015

Key resources table

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit monoclonal anti-MYC [Y69] Abcam Cat# ab32072, RRID:AB_731658
Anti-EBF-1 Antibody Millipore Cat# AB10523, RRID:AB_2636856
Anti-Early B-cell factor (EBF1) Antibody Sigma-Aldrich Cat# ABE1294, RRID:AB_2893472
Rabbit anti-EBF1 (Boller et al., 2016) N/A
TCF1 (C46C7) Rabbit mAb antibody CST Cat# 2206, RRID:AB_2199300
LEF1 (D6J2W) Rabbit mAb CST Cat# 76010, RRID:AB_2799877
Maml1 (D3K7B) Rabbit mAb CST Cat# 12166, RRID:AB_2797838
Cleaved Notch1 (Val1744) (D3B8) Rabbit mAb CST Cat# 4147, RRID:AB_2153348
Caspase-3 Antibody CST Cat# 9662, RRID:AB_331439
Annexin V Recom Horizon V450 50 test antibody BD Cat# 560506, RRID:AB_2869356
Monoclonal Anti-β-Actin antibody, clone AC-74 Sigma-Aldrich Cat# A5316, RRID:AB_476743
Calnexin (C5C9) Rabbit mAb antibody CST Cat# 2679, RRID:AB_2228381
GAPDH (D16H11) XP Rabbit mAb antibody CST Cat# 5174, RRID:AB_10622025
Rabbit polyclonal anti-H3 acetyl-K27 Active Motif Cat# 39133, RRID:AB_2561016
Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb CST Cat# 9733, RRID:AB_2616029
Rabbit polyclonal anti-H3 mono methyl-K4 Abcam Cat# ab8895, RRID:AB_306847
Rabbit anti-SMC1 Antibody, Affinity Purified Bethyl Cat# A300–055A, RRID:AB_2192467
Rabbit polyclonal anti-CTCF Millipore Cat# 07–729, RRID:AB_441965
YY1 antibody (pAb) Active Motif Cat# 61779, RRID:AB_2793763
Cas9 (7A9-3A3) antibody CST Cat# 14697, RRID:AB_2750916
Rabbit Anti-Lamin B1 Polyclonal Antibody Abcam Cat# ab16048, RRID:AB_443298
Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Cat# A10042, RRID:AB_2534017
Goat Anti-Rabbit IgG, H & L Chain Specific Peroxidase Conjugate antibody Millipore Cat# 401315, RRID:AB_437787
Goat Anti-Mouse IgG, H & L Chain Antibody, Peroxidase Conjugated Millipore Cat# 401215, RRID:AB_10682749
Bacterial and virus strains
One Shot Stbl3 Chemically Competent E.coli Thermo Cat# C737303
Chemicals, peptides, and recombinant proteins
Trypsin (2.5%) Gibco Cat# 15090-046
gamma-Secretase Inhibitor XXI (compound E) Calbiochem Cat# 565790
FuGene HD Promega Cat# E2311
Penicillin-Streptomycin Corning Cat# 30-002-CI
MEM Non-Essential Amino Acids Gibco Cat# 11140-050
Sodium Pyruvate Gibco Cat# 11360-070
2-mercaptoethanol Sigma Cat# M3148
RPMI 1640 Corning Cat# 10-040-CM
DMEM Corning Cat# 10-013-CV
Dulbecco’s Phosphate-Buffered Salt Solution 1X Corning Cat# 21031CV
HyClone Fetal bovine serum Thermo Fisher Scientific Cat# SH30070.03
L-glutamine Corning Cat# 25-005-CI
Polybrene Sigma-Aldrich Cat# H9268
Gibco Puromycin Dihydrochloride (10 mg/mL) Thermo Cat# A1113803
Complete Protease Inhibitor Cocktail Tablets Roche Cat# 11697498001
Complete Mini EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001
Recombinant Protein G Agarose Invitrogen Cat# 15920-010
Lithium Chloride, 8M Sigma-Aldrich Cat# 7447-41-8
Sodium bicarbonate Sigma-Aldrich Cat#144-55-8
RNase A Roche Cat# 10109169001
Proteinase K Invitrogen Cat# 25530-049
Pierce™ 16% Formaldehyde Thermo Cat# 28908
EGS Thermo Cat# 21565
Glycine Invitrogen Cat# 15527-013
MboI NEB Cat# R0147
SalI-HF NEB Cat# R3138S
AscI NEB Cat# R0558S
NEBNext End Repair Module NEB Cat# E6050
Klenow Fragment (3’ to 5’ exo-) NEB Cat# M0212
CIP NEB Cat# M0290
TO-PRO3 Ready Flow Reagent Thermo Cat# R37170
Hygromycin B Gold 1 g (10 × 1 ml) Invivogen Cat# ant-hg-1
Biotin-14-dATP 200 μl (1 mM) Jena Bioscience Cat# NU-835-BIO14-S
Maxima H Minus Reverse Transcriptase (200 U/μL) Thermo Cat# EP0752
T4 DNA Ligase NEB Cat# M0202L
DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210S
Triton X-100 Roche Cat# 10789704001
BSA, 50mg/ml Invitrogen Cat# AM2616
SurePAGE, Bis-Tris, 10×8, 4–12%, 15 wells GenScript Cat# M00654
MES SDS Running Buffer Powder GenScript Cat# M00677
PageRuler Prestained Protein Ladder, 10 to 180 kDa Thermo Cat# 26616
PageRuler Plus Prestained Protein Ladder, 10 to 250 kDa Thermo Cat# PI26619
Tween 20 BIO-RAD Cat# 170-6531
Protein A Magnetic Beads Pierce Cat# 88846
Dynabeads MyOne Streptavidin C1 Invitrogen Cat# 65001
Dynabeads Protein G for Immunoprecipitation Invitrogen Cat# 10003D
Phenol-chloroform-isoamyl (PCI) Invitrogen Cat# 15593049
Dimethylformamide Sigma-Aldrich Cat# D4551
Power SYBR™ Green PCR Master Mix Applied Biosystems Cat# 4367659
Tris-HCI, pH 7.5, 1M Invitrogen Cat# 15567-027
Tris-HCI, pH 8.0, 1M Invitrogen Cat# 15568-025
EDTA, pH 8.0, 0.5M Invitrogen Cat# 15575-020
Sodium Chloride Fisher BioReagents Cat# 7647-14-5
MgCl2, 1M Thermo Cat# AM9530G
NP-40 (Igepal CA-630) Sigma Cat# I8896
Sodium deoxycholate Sigma-Aldrich Cat# D6750
SDS solution, 10% Invitrogen Cat# 15553-027
Geneticin Selective Antibiotic (G418) (50 mg/mL) Thermo Cat# 10131035
Doxycycline Sigma Cat# D9891
Gibco Blasticidin S HCl (10 mg/mL) Thermo Cat# A1113903
Phusion PCR Master Mix NEB Cat# M0531
Phusion Flash High-Fidelity PCR Master Mix Thermo Cat# F548S
NEBNext High-Fidelity 2X PCR Master Mix NEB Cat# M0541
AMPure XP Beckman Coulter Cat# A63881
SuperScript III Reverse Transcriptase Invitrogen Cat# 18080093
Gateway™ LR Clonase™ II Enzyme mix Invitrogen Cat# 11791020
Gateway™ BP Clonase™ II Enzyme mix Invitrogen Cat# 11789020
poly-L-lysine-treated glass slides Thermo Cat# P4981-001
Polyvinylsulfonic acid (PVSA) Sigma Aldrich Cat# 278424
20x SSC Buffer Corning Cat# 46-020-CM
Slowfade Invitrogen Cat# 336936
Critical commercial assays
CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7571
DC Protein Assay Reagents Package Bio-rad Cat# 5000116
QIAquick PCR Purification Kit QIAGEN Cat# 28106
MinElute Reaction Cleanup Kit QIAGEN Cat# 28204
DNeasy Blood & Tissue Kit QIAGEN Cat# 69504
RNeasy Plus Mini Kit QIAGEN Cat# 74136
RNeasy Plus Micro Kit QIAGEN Cat# 74034
SeqCap Adapter Kit A Roche Cat# 7141530001
KAPA Library Quant Kit Roche Cat# KK4824
ZymoPURE Plasmid Miniprep Kit 100 preps Zymo Cat# D4210
Zymoclean Gel DNA Recovery Kit Zymo Cat# D4007
NEBuilder HiFi DNA Assembly Cloning Kit NEB Cat# E5520S
NEBNext Ultra II DNA Library Prep Kit NEB Cat# E7645S
HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S
SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian Takara Cat# 634873
NucleoBond Xtra Maxi EF Takara Cat# 740424
ECL Prime Western Blotting Detection Reagents Cytiva Cat# RPN2232
D1000 ScreenTape Agilent Cat# 5067-5582
D1000 Reagents Agilent Cat# 5067-5583
High Sensitivity D1000 ScreenTape Agilent Cat# 5067-5584
High Sensitivity D1000 Reagents Agilent Cat# 5067-5585
Genomic DNA ScreenTape Agilent Cat# 5067-5365
Genomic DNA Reagents Agilent Cat# 5067-5366
RNA ScreenTape Agilent Cat# 5067-5576
RNA ScreenTape Ladder Agilent Cat# 5067-5578
RNA ScreenTape Sample Buffer Agilent Cat# 5067-5577
Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32851
Qubit ssDNA Assay Kit Invitrogen Cat# Q10212
Arima-HiC Kit (8 Reactions) Arima Cat# A510008
Accel-NGS 2S Plus DNA Library Kit (24 rxns) Swift Cat# 21024
2S SET A INDEXING KIT (12 INDICES, 48 RXNS) Swift Cat# 26148
NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) NEB Cat# E7600S
NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 2) NEB Cat# E7780S
Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat# FC-131-2001
Illumina Tagment DNA Enzyme and Buffer Kit Illumina Cat# 20034197
Nextseq 500/550 high output kit v2.5 (75 cycles) Illumina Cat# 20024906
NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles) Illumina Cat# 20028319
Deposited data
Raw and analyzed data This study GSE173872
MB157 HiChIP (Petrovic et al., 2019) GSE116869
Experimental models: Cell lines
HPB-ALL DSMZ Cat# ACC 483
KOPTK1 (Wang et al., 2014) N/A
Granta-519 (Ryan et al., 2017) N/A
DND41 DSMZ Cat# ACC 525
MB157 ATCC Cat# CRL-7721
HEK293T ATCC Cat# CRL-3216
Oligonucleotides
Primer: EEF1A1 qPCR forward: TTGTCGTCATTGGACACGTAG (Petrovic et al., 2019) N/A
Primer: EEF1A1 qPCR reverse: TGCCACCGCATTTATAGATCAG (Petrovic et al., 2019) N/A
Primer: MYC qPCR forward: ACCCTCTCAACGACAGCAGC (Petrovic et al., 2019) N/A
Primer: MYC qPCR reverse: ACTCCGTCGAGGAGAGCAGA (Petrovic et al., 2019) N/A
Primer: CD300A qPCR forward: GCGGCCAAGACCTCAACAA This study N/A
Primer: CD300A qPCR reverse: TGAGTTCACCACCTCCTCAGT This study N/A
Primer: DTX1 qPCR forward: ATGGAGCGACTGGTCACAGC This study N/A
Primer: DTX1 qPCR reverse: CCGTAGATGGCCTTGCAGGT This study N/A
Primer: CR2 qPCR forward: CACACACCGGGAGTTCCTTA This study N/A
Primer: CR2 qPCR reverse: ACAACGGATGGTGCTCTCTC This study N/A
Primer: LEF1 qPCR forward: TAATGCACGTGAAGCCTCAGCA This study N/A
Primer: LEF1 qPCR reverse: CACTCAGCAACGACATTCGCTC This study N/A
Primer: TCF7 qPCR forward: CCAACCATCAAGAAGCCCCT This study N/A
Primer: TCF7 qPCR reverse: TGTGCACTCTGCAATGACCT This study N/A
Primer: CD79A qPCR forward: GCACCAAGAACCGAATCATC This study N/A
Primer: CD79A qPCR reverse: CTTCTCGTTCTGCCATCGTT This study N/A
Primer: pDONR221-LEF1 PCR forward: GGGGACAAGTTTGTACAAAAAAGCAGGCTTCATGCCCCAACTCTCCGGAGGA This study N/A
Primer: pDONR221-LEF1 PCR reverse: GGGGACAAGTTTGTACAAAAAAGCAGGCTTCATGCCCCAACTCTCCGGAGGA This study N/A
Primer: pDONR221-TCF7 PCR forward: GGGGACAAGTTTGTACAAAAAAGCAGGCTTCAGATCGGCCACCATGTATCC This study N/A
Primer: pDONR221-TCF7 PCR reverse: GGGGACCACTTTGTACAAGAAAGCTGGGTCGttatctagagcactgtcatcgg This study N/A
Primer: TRE3G-EBF1-puro PCR forward: TACCCTCGTAAAACCGGTCGATGTTTGGGATTCAGGAAAG This study N/A
Primer: TRE3G-EBF1-puro PCR reverse: GTACAAGAAAGCTGGGTCGGTCACATAGGAGGAACAATC This study N/A
sgRNA: MYC targeting sequence E3g5: GCGTGACCAGATCCCGGAGT This study N/A
sgRNA: LEF1 targeting sequence g3: CCCTCCTACTCGAGTTATTC This study N/A
sgRNA: TCF7 targeting sequence g5: TGTTCGTAGAGAGAGAGTTG This study N/A
sgRNA: EBF1 targeting sequence g7: TCTCATGTGTGAGCAAGACT This study N/A
Secondary Oligopaint probe: /5Alex488N/CACACGCTCTTCCGTTCTATGCGACGTCGGTG/3AlexF488N/ (Beliveau et al., 2018) N/A
Secondary Oligopaint probe: /5ATTO565N/ACACCCTTGCACGTCGTGGACCTCCTGCGCTA/3ATTO565N/ (Beliveau et al., 2018) N/A
Secondary Oligopaint probe: /5Alex647N/TGATCGACCACGGCCAAGACGGAGAGCGTGTG/3AlexF647N/ (Beliveau et al., 2018) N/A
Recombinant DNA
LentiV_Cas9_puro (Grevet et al., 2018) Addgene Cat# 108100
LRG2.1 (Grevet et al., 2018) Addgene Cat# 108098
LRCherry2.1 (Grevet et al., 2018) Addgene Cat# 108099
Gateway pDONR221 Invitrogen Cat# 12536017
pInducer20 Addgene Cat# 44012
pINDUCER21 (ORF-EG) Addgene Cat# 46948
pENTR221-TCF7 Addgene Cat# 79498
pDONR221-EBF1 DNASU Cat# HsCD00296820
pDONR221-LEF1 This study N/A
pDONR221-TCF7 This study N/A
pInducer20-LEF1 This study N/A
pInducer20-TCF7 This study N/A
pInducer20-EBF1 This study N/A
pInducer21-EBF1 This study N/A
TRE3G-TRF1-puro (Dilley et al., 2016) N/A
CMV-rtTA3G-blast (Dilley et al., 2016) N/A
TRE3G-EBF1-puro This study N/A
Software and algorithms
Benchling N/A https://www.benchling.com
BEDTools v2.25.0 (Quinlan and Hall, 2010) https://bedtools.readthedocs.io/en/stable;
RRID:SCR_006646
biomaRt v2.28.0 (Durinck et al., 2005) https://www.rdocumentation.org/packages/biomaRt/versions/2.28.0; RRID:SCR_006442
BWA v0.7.13 (Li and Durbin, 2009) http://bio-bwa.sourceforge.net; RRID:SCR_010910
DESeq2 v1.10.1 (Love et al., 2014) https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID:SCR_015687
FlowJo v9.7.7 FlowJo LLC https://www.flowjo.com; RRID:SCR_008520
ggplot2 v2.2.1 (Wickham, 2009) https://ggplot2.tidyverse.org; RRID:SCR_014601
HiC-Pro v2.5.0 (Servant et al., 2015) https://github.com/nservant/HiC-Pro
HOMER v4.8 (Heinz et al., 2010) http://homer.ucsd.edu/homer; RRID:SCR_010881
JASPAR (Sandelin et al., 2004) http://jaspar.genereg.net; RRID:SCR_003030
Juicer tools v1.7.6 (Durand et al., 2016b) https://github.com/aidenlab/juicer
Juicebox v1.0 (Durand et al., 2016a) https://www.aidenlab.org/juicebox
MACS v2.0.9 (Zhang et al., 2008) https://github.com/taoliu/MACS; RRID:SCR_013291
Mango v1.2.0 (Phanstiel et al., 2015) https://github.com/dphansti/mango
MEME v4.11.1 (Bailey et al., 2015) http://meme-suite.org/index.html; RRID:SCR_001783
MSigDB v6.1 (Liberzon et al., 2015) http://software.broadinstitute.org/gsea/msigdb/index.jsp; RRID:SCR_003199
normR v1.6.0 (Helmuth and Chung, 2018) https://bioconductor.org/packages/release/bioc/html/normr.html; RRID:SCR_006442
Picard v2.1.0 Broad Institute https://broadinstitute.github.io/picard; RRID:SCR_006525
pheatmap v 1.0.10 R. Kodle https://github.com/raivokolde/pheatmap; RRID:SCR_016418
RepeatMasker AFA Smit, R Hubley, P. Green http://www.repeatmasker.org; RRID:SCR_012954
SAMTools v1.3 (Li et al., 2009) http://samtools.sourceforge.net; RRID:SCR_002105
STAR v2.5 (Dobin et al., 2013) https://github.com/alexdobin/STAR; RRID:SCR_015899
Sushi v1.18.0 (Phanstiel et al., 2014) https://bioconductor.org/packages/release/bioc/html/Sushi.html; RRID:SCR_006442
Trim Galore v0.4.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/projects/trim_galore; RRID:SCR_011847
UCSC tools v329 (Kent et al., 2010) https://github.com/ucscGenomeBrowser/kent