KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-H2AX-p-S139 antibody | BD Biosciences | clone N1-431, cat 560443, RRID: AB_1645592 |
| HA antibody | Biolegend | clone HA.11, cat 901514, RRID: AB_2565336 |
| Tubulin | Santa Cruz | clone 6A204, cat sc-69969, RRID: AB_1118882 |
| Bacterial and virus strains | ||
| pSLIK-A3A lentivirus | Vector obtained from addgene, cloned in Green Lab, lentivirus generated in Green Lab | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Doxycycline | Sigma | D9891-1G |
| PowerSYBR Green PCR Master Mix | AppliedBiosystems | 43-676-59 |
| Uracil DNA glycosylase | NEB | M0280 |
| Critical commercial assays | ||
| RNeasy kit | Qiagen | N/A |
| RNA-to-cDNA kit | Invitrogen | N/A |
| Deposited data | ||
| OK-Seq raw data from DT40 cells | GEO | Accession number GSE196761 |
| DT40 genome sequencing raw data | European Nucleotide Archive | Accession number PRJEB50626 |
| Replication timing information | Replication Domain database www.replicationdomain.com | Int98808223 data set |
| Replication fork direction processing data from DT40 cells | https://github.com/CL-CHEN-Lab/OK-Seq. | N/A |
| Experimental models: Cell lines | ||
| DT40 cells | Szuts lab | N/A |
| Oligonucleotides | ||
| 5’-FAM TGAGGAATGAAGTTGATTUAA ATGTGATGAGGTGA | IDT | TU Control oligo for deaminase reaction |
| 5’-FAM TGAGGAATGAAGTTGATTCAAA TGTGATGAGGTGA |
IDT | TC oligo for deaminase reaction |
| Recombinant DNA | ||
| pSLIK-A3A lentivector | Addgene | 25735 |
| Software and algorithms | ||
| Prism | GraphPad | version 9 |
| Via7 | Invitrogen | N/A |
| FlowJo | version 10.7.1 | N/A |
| IsoMut | (Pipek et al. 2017) | N/A |
| MuTect2 | GATC Toolkit https://gatk.broadinstitute.org | N/A |
| Bismark | (Krueger and Andrews 2011) | N/A |