KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-RPA32/RPA2 antibody (ab10359) | Abcam | Cat# ab10359; RRID: AB_297095 |
| RP105 (Purified Rat Anti-Mouse CD180) | BD Biosciences | Cat# 552128; RRID: AB_394343 |
| Purified Hamster Anti-Mouse TCR beta chain | BD Biosciences | Cat# H57–597; RRID: AB_394679 |
| Purified Hamster Anti-Mouse CD28 | BD Biosciences | Cat# 553294; RRID: AB_394763 |
| Anti-phospho-Histone H3 (Ser10) Antibody | Millipore-Sigma | Cat# 06–570; RRID: AB_310177 |
| Goat anti-Rabbit IgG (H+L) Alexa Fluor 488 | ThermoFisher | Cat# A-11008; RRID: AB_143165 |
| Mouse IgG1 anti-BrdU | BD Biosciences | Cat# 347580; RRID: AB_400326 |
| Rat anti-BrdU | Accurate chemical | Cat# OBT0030; RRID: AB_2313756 |
| Mouse IgG2a anti-ssDNA | Chemicon | Cat# MAB3034; RRID: AB_94645 |
| Alexa Fluor 594 donkey anti-rat | ThermoFisher | Cat# A21209; RRID: AB_2535795 |
| Alexa Fluor 488 goat anti mouse IgG1 | ThermoFisher | Cat# A21121; RRID: AB_2535764 |
| Alexa Fluor 647 goat anti mouse IgG2a | ThermoFisher | Cat# A21241; RRID: AB_2535810 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| HU | Millipore-Sigma | Cat# H8627 |
| TRIzol Reagent | Thermo Fisher | Cat# 15596026 |
| EdU (5-ethynyl-2′-deoxyuridine) | Thermo Fisher | Cat# A10044 |
| 5-Ethynyl-2′-deoxycytidine, (EdC) | Millipore-Sigma | Cat# T511307 |
| AZ20 (ATR inhibitor) | Selleckchem | Cat# S7050 |
| Palbociclib (PD-0332991) HCl | Selleckchem | Cat# S1116 |
| Roscovitine (Seliciclib,CYC202) | Selleckchem | Cat# S1153 |
| PHA-767491 | Selleckchem | Cat# S2742 |
| Biotin Azide (PEG4 carboxamide-6-Azidohexanyl Biotin) | Invitrogen | Cat# B10184 |
| Exonuclease T (ExoT) | NEB | Cat# M0265S |
| Exonuclease VII (ExoVII) | NEB | Cat# M0379S |
| Klenow Fragment (3′→5′ exo-) | NEB | Cat# M0212S |
| Quick Ligation Kit | NEB | Cat# M2200S |
| USER enzyme | NEB | Cat# M5505S |
| KAPA HiFi HotStart ReadyMix (2X) | KAPA Biosystems | Cat# KK2600 |
| Lipopolysaccharide (LPS) | Millipore-Sigma | Cat# L-2630 |
| IL-4 | Millipore-Sigma | Cat# I1020 |
| UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) | Invitrogen | Cat# 15593031 |
| Critical Commercial Assays | ||
| Click-IT Nascent RNA Capture Kit | Invitrogen | Cat# C10365 |
| Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit | Invitrogen | Cat# C10424 |
| Anti-CD43 (Ly-48) MicroBeads mouse | Miltenyi Biotech | Cat# 130–049-80 |
| NEBNext rRNA Depletion kit | NEB | Cat# E6310S |
| KAPA Library Quantification Kit | Kapa Biosystems | Cat# KK4824 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE116321 |
| HCT116 MNase-seq | Guzman and D’Orso, 2017 | GEO: GSE89871 |
| B cell MNase-seq | Kieffer-Kwon et al., 2017 | GEO: GSE82144 |
| OK-seq: HeLa | Petryk et al., 2016 | SRA: SRP065949 |
| ERFS hotspots | Barlow et al., 2013 | GEO: GSE43504 |
| Experimental Models: Cell Lines | ||
| HCT116 | Gift from Masato Kanemaki | |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6NCr | Charles River | Strain code# 027 |
| Mouse: CAST/EiJ | Jackson Laboratory | Stock No: 000928 |
| Oligonucleotides | ||
| TruSeq barcoded primer, 5′-Phos- CAAGCAGAAGACGGCA TACGAGATNNNNNNGTGACTGG AGTTCAGACGTGTGCT CTTCCGATC*T-5′ |
Canela et al., 2017 | N/A |
| TruSeq mulitplex primer, 5′-Phos- AATGATACGG CGACC ACCGAGATCTACACTCTTTCCCTA CACGACGCTCTTC CGATC |
Canela et al., 2017 | N/A |
| END-seq hairpin adaptor 1, 5′-Phos-GATCGGAAGAGC GTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT] UUACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ |
Canela et al., 2017 | N/A |
| END-seq hairpin adaptor 2, | Canela et al., 2017 | |
| OK-seq Adaptor 1 - Watson, 5′-ACA CTC TTT CCC TAC ACG ACG CTC TTC C-3′ |
Petryk et al. 2016 | |
| OK-seq Adaptor 1- Crick, 5′- NNN NNN G GAA GAG CGT CGT GTA GGG AAA GAG TG-3′ |
Petryk et al. 2016 | |
| OK-seq Adaptor 2- Watson, 5′ AGA TCG GAA GAG CAC ACG TCT GAA CTC CAG TCA [ddC]-3′ |
Petryk et al. 2016 | |
| OK-seq Adaptor 2- Crick, 5′-TGA CTG GAG TTC AGA CGT GTG CTC TTC CGA TCT NNN NNN [DDC]-3′ |
Petryk et al. 2016 | |
| PE PCR Primer 1.0 Meyer - Forward, 5′-ATGATACGGC GACCACCGAGATCTACACTCTTTCCCTACACGACGC TCTTCC-3′ |
Petryk et al. 2016 | |
| TruSeq PCR Primer - Reverse, 5′-CAAGCAGAAGACGG CATACGAGAT-INDEX-GTGACTGGAGTTCAGACGTGT GCTCTTCCGATCT-3′ |
Petryk et al. 2016 | |
| Software and Algorithms | ||
| Bowtie 1.1.2 | Langmead et al., 2009 | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/ |
| Bowtie 2.3.4.1 | Langmead and Salzberg, 2012 | https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/ |
| MACS 1.4.3 | Zhang et al., 2008 | https://pypi.org/project/MACS/1.4.3/ |
| UCSC Database | Karolchick et al., 2004 | https://genome.ucsc.edu |
| UCSC Genome Browser | Kent et al., 2002 | https://genome.ucsc.edu |
| Bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools2 |
| Samtools | Li et al., 2009 | https://github.com/samtools/samtools |
| R | https://www.r-project.org/ | |
| FlowJo (10.1) | FlowJo | https://www.flowjo.com/solutions/flowjo/ |