Key resources table.
| Reagent type (Species or Source) |
Designation | Source | Identifier | Add. info |
|---|---|---|---|---|
| Antibody | Anti-phospho-Histone H2A.X (Ser139) (mouse monoclonal) | Millipore | Cat# JBW301; RRID:AB_309864 | (1:5000 - 1:10000) |
| Antibody | Anti-Tubulin (mouse monoclonal) | Sigma | Cat# T-5168 RRID:AB_477585 |
(1:5000) |
| Antibody | Anti-p53 (1CA2) (mouse monoclonal) | Cell Signaling | Cat# 2524 RRID:AB_331743 |
(1:2000) |
| Antibody | Anti-Vinculin (rabbit polyclonal) | Cell Signaling | Cat# 4650 RRID:AB_10559207 |
(1:2000) |
| Antibody | Anti-Top2b (rabbit polyclonal) | Novus | Cat# NB100-10842 RRID:AB_1522570 |
(1:5000) |
| Antibody | Anti-Rabbit Li-Cor (goat polyclonal) | Li-Cor | Cat# 926–32211; RRID:AB_621843 | (1:10000) |
| Antibody | Anti-mouse IgG1 Alexa 488 (goat polyclonal) | Invitrogen | Cat# A-21121; RRID:AB_141514 | (1:10000) |
| Antibody | Anti-H2AX (rabbit polycolonal) | Abcam | Cat# ab11175 RRID:AB_297814 |
(1:5000) |
| Chemical compound, Drug | Etoposide | Sigma | Cat# E1383 | 10–50 μM |
| Chemical compound, Drug | Bortezomib | Millipore | Cat# 179324-69-7 | 1–5 μM |
| Chemical compound, Drug | MG132 | Sigma | Cat# 1211877-36-9 | 10 μM |
| Chemical compound, Drug | Camptothecin | Sigma | Cat# 7689-03-4 | 12.5 μM |
| Chemical compound, Drug | Ixaomib | Selleckchem | Cat# S2180 | 10 μM |
| Chemical compound, Drug | Eponomicin | Sigma | Cat# 134381-21-8 | 2 μM |
| Chemical compound, Drug | Doxycycline hyclate | Sigma | Cat# D9891 | 1 μg/ml |
| Chemical compound, Drug | Imatinib mesylate (STI571) | Selleckchem | Cat# S1026 | |
| Cell Line (M. musculus) | pre-B cell lines | Bredemeyer et al., 2006 | ||
| Cell Line (M. musculus) | RNF4-/- MEFs | Generated by Gary Lyons, Hu et al., 2010 | ||
| Biological Sample (M. musculus) | Primary splenic B-cells | Freshly isolated from M. musculus spleen | ||
| Strain (M. musculus) | C57BL/6NCr mice (WT) | Charles River | Strain code# 027 | |
| Strain (M. musculus) | Conditional BRCA1-Δ11f/f CD19-cre expressing mice | NCI mouse repository | ||
| Strain (M. musculus) | H2AX-/- mice | Celeste et al., 2002 | ||
| Strain (M. musculus) | Conditional Lig4f/f expressing ERT2-Cre mice | Provided by P. Mckinnon | ||
| Strain (M. musculus) | ATM-/- mice | Provided by A. Wynshaw-Boris | ||
| Strain (M. musculus) | Conditional RNF4 f/f mice | Provided by S. Bunting | ||
| Strain (M. musculus) | Conditional BRCA2 f/f CD19-cre expressing mice | Provided by S. Sharan | ||
| Strain (M. musculus) | PolQ-/- mice | Provided by A. D'Andrea | ||
| Recombinant DNA reagent | YFPu Degron reporter (plasmid) | Provided by A. Weissman Bence et al., 2005; Bence et al., 2001 |
(0.5 ng/μL) | |
| Peptide, recombinant protein | Lipopolysaccharide (LPS) | Sigma | Cat# L-2630 | 25 μg/ml |
| Peptide, recombinant protein | IL-4 from mouse, Interleukin-4, recombinant | Sigma | Cat# I-1020 | 5 ng/ml |
| Peptide, recombinant protein |
RP105 | BD Biosciences | Cat # 552128 | 0.5 μg/ml |
| Peptide, recombinant protein | Cy3-labeled (CCCTAA) peptide nucleic acid probe | PNA Bio | Cat# F1002 | |
| Peptide, recombinant protein | Puregene Proteinase K solution | Qiagen | Cat# 19133 | 170 μL |
| Peptide, recombinant protein | Puregene RNaseA | Qiagen | Cat# 19101 | 50 μL |
| Peptide, recombinant protein | T4 DNA polymerase | NEB | Cat# M0203L | 15 U |
| Peptide, recombinant protein | Klenow fragment | NEB | Cat# M0210M | 5 U |
| Peptide, recombinant protein | T4 polynucleotide kinase | NEB | Cat# M0201L | 15 U |
| Peptide, recombinant protein | Klenow exo-fragment | NEB | Cat# M0212M | 15 U |
| Peptide, recombinant protein |
Quick Ligase | NEB | Cat# M2200L | |
| Peptide, recombinant protein |
USER enzyme | NEB | Cat# M5508L | |
| Peptide, recombinant protein |
beta-agarase I | NEB | Cat# M0392S | 1.5 μL |
| Commercial Assay Kit | CHEF Mammalian Genomic DNA plug kit | Bio-Rad | Cat# 1703591 | |
| Commercial Assay Kit |
Click-IT EdU Alexa Fluor 488 Flow Cytometry Assay Kit |
ThermoFisher | Cat# C10425 | |
| Commercial Assay Kit |
KAPA Library Quantification Kit | Kapa Biosciences | Cat# KK4824 | |
| Commercial Assay Kit | Celltiter-Glo Cell Viability Assay Kit | Promega | Cat# G7571 | |
| Other | Streptavidin beads MyOne C1 | ThermoFisher | Cat# 650–01 | 35 μL |
| Other | Anti-CD43 (Ly-48) MicroBeads (mouse) | Miltenyi Biotech | Cat# 130-049-80 | |
| Other | Glycogen (20 mg/ml) | Roche | Cat# 10901393001 | 1 μL |
| Other | Kapa HiFi Hot Start Ready mix |
Kapa Biosciences | Cat# KK2502 | |
| Other | Agencourt AM Pure XP beads |
Beckman Coulter | Cat# A63881 | |
| Other | IrysPrep Lysis Buffer |
BioNano Genomics | Cat# 20270 | |
| Other | X-tremeGene 9 Transfection Reagent | Sigma | Cat # XTG9-RO | |
| Sequence-based reagent | END-seq hairpin adaptor 1, 5′-Phos-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ | Canela et al., 2016 | END-seq sequence adapter | |
| Sequence-based reagent | END-seq hairpin adaptor 2, 5′-Phos-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC∗T-3′ | Canela et al., 2016 | END-seq sequence adapter | |
| Sequence-based reagent | TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T | Canela et al., 2019 | END-seq sequence primer | |
| Sequence-based reagent | TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | Canela et al., 2019 | END-seq sequence primer | |
| Software | Prism (7) | GraphPad |
https://www.graphpad.com/scientific-software/prism/
RRID:SCR_002798 |
|
| Software | Bowtie 1.1.2 |
Langmead et al., 2009 |
https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/
RRID:SCR_005476 |
|
| Software | MACS 1.4.3 | Zhang et al., 2008 | https://pypi.python.org/pypi/MACS/1.4.3 | |
| Software | UCSC database | Karolchik et al., 2004 |
https://genome.ucsc.edu
RRID:SCR_005780 |
|
| Software | UCSC Genome Browser | Kent et al., 2002 |
https://genome.ucsc.edu
RRID:SCR_005780 |
|
| Software | Bedtools | Quinlan and Hall, 2010 |
https://github.com/arq5x/bedtools2
RRID:SCR_006646 |
|
| Software | Samtools | Li et al., 2009 |
https://github.com/samtools/samtools
RRID:SCR_002105 |
|
| Software | Knight-Ruiz algorithm |
Rao et al., 2014 |
https://academic.oup.com/imajna/article-lookup/
DOI: 10.1093/imanum/drs019 |
|
| Software | R | R Development Core Team (2008) |
https://www.r-project.org/
RRID:SCR_001905 |
|
| Software | FlowJo (10.1) | FlowJo LLC |
https://www.flowjo.com/
RRID:SCR_008520 |
|
| Software | Metapher ISIS | Metapher Systems | ||
| Software | hiSKY 7.2.7 | ADS Biotech | ||