Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Mus musculus, Male) |
A9 | ATCC, (Tattersall and Bratton, 1983) PMID: 6602222 |
RRID:CVCL_3984 | Verified as mycoplasma- negative by PCR |
| Cell line (Mus musculus) |
NIH-3T3 | ATCC | RRID:CVCL_0594 | Verified as mycoplasma- negative by PCR |
| Cell line (Homo sapiens) |
NB-324K | (Tattersall and Bratton, 1983) PMID: 6602222 |
RRID:CVCL_U409 | Verified as mycoplasma- negative by PCR |
| Cell line (Mus musculus) |
EL4 | ATCC, (Tattersall and Bratton, 1983) PMID: 6602222 |
RRID:CVCL_0255 | Verified as mycoplasma- negative by PCR |
| Cell line (Rattus norvegicus) |
F111 | Fischer Rat Fibroblasts; (Freeman et al., 1975) |
RRID:CVCL_6C52 | Verified as mycoplasma- negative by PCR |
| Antibody | NS1 | Salome and Pintel, unpublished |
2C9b | anti-mouse; Usage per sample: ChIP: 6 µg Immunofluorescence: 2 µg IB: 2 µg |
| Antibody | γ−Η2ΑX | EMD Millipore | EMD Millipore:05–636 | anti-mouse; Usage per sample: ChIP: 5 µg |
| Antibody | γ−Η2ΑX | Abcam:ab11174 | RRID:AB_297813 | anti-rabbit; Usage per sample: ChIP: 5 µg Immunofluorescence: 2 µg IB: 2 µg |
| Antibody | BRCA1 | Thermo Fisher Scientific:17F8 |
RRID:AB_557804 | anti-mouse; Usage per sample: ChIP: 5 µg |
| Antibody | FANCD2 | Bethyl Laboratories: a302-174A |
RRID:AB_1659803 | anti-rabbit; Usage per sample: Immunofluorescence: 2 µg |
| Antibody | NR5A2 | Abcam:ab189876 | RRID: AB_2732890 | anti-rabbit; Usage per sample: Immunofluorescence: 2 µg |
| Antibody | IgG | Cell Signaling | Cell Signaling:5415S | mouse; Usage per sample: ChIP: 5 µg |
| Antibody | AF 488 | Life Technologies: A11034 |
RRID:AB_2576217 | anti-rabbit secondary; Usage per sample: Immunofluorescence: 1 µg |
| Antibody | AF 568 | Life Technologies: A11031 |
RRID:AB_144696 | anti-mouse secondary; Usage per sample: Immunofluorescence: 1 µg |
| Antibody | AF 555 | Life Technologies: A27039 |
RRID:AB_2536100 | anti-rabbit secondary; Usage per sample: Immunofluorescence: 1 µg |
| Antibody | AF 647 | Life Technologies: A32728 |
RRID:AB_2633277 | anti-mouse secondary; Usage per sample: Immunofluorescence: 1 µg |
| Recombinant DNA reagent |
Lenti-CRISPRv2 | Addgene; (Sanjana et al., 2014) PMID: 25075903 |
Addgene plasmid 52961 | |
| Recombinant DNA reagent |
pgRNA-humanized | Addgene; (Qi et al., 2013) PMID: 23452860 |
Addgene plasmid 44248 | |
| Peptide, recombinant protein |
HindIII | New England Biolabs |
NEB:R0104 | |
| Peptide, recombinant protein |
NlaIII | New England Biolabs |
NEB:R0125 | |
| Peptide, recombinant protein |
T4 DNA Ligase | New England Biolabs |
NEB:M0202 | |
| Commercial assay or kit |
FISH Tag DNA Multicolor Kit |
Thermo Fisher Scientific |
Thermo Fisher Scientific: F32951 |
|
| Commercial assay or kit |
QIAquick PCR purification kit |
Qiagen | Qiagen:28106 | |
| Commercial assay or kit |
NEBNext Ultra II Library Prep Kit for Illumina |
New England Biolabs |
NEB:E7645 | |
| Commercial assay or kit |
Trevigen Comet Assay Kit |
Trevigen | Trevigen: 4250–050 K | |
| Commercial assay or kit |
StemCell | EasySep Human CD4+ T Cell Enrichment Kit |
StemCell:19052 | |
| Chemical compound, drug |
Hydroxyurea | Sigma Aldrich | Sigma Aldrich:H8627 | |
| Chemical compound, drug |
Doxorubicin | Sigma Aldrich | Sigma Aldrich:D1515 | |
| Chemical compound, drug |
Bovine Serum Albumin |
Sigma Aldrich | Sigma Aldrich:A2153 | |
| Chemical compound, drug |
ProLong Diamond Antifade Mountant with DAPI |
Thermo Fisher Scientific |
Thermo Fisher Scientific: P36966 |
|
| Chemical compound, drug |
Hoechst 33342 | Thermo Fisher Scientific |
Thermo Fisher Scientific: 62249 |
|
| Software, algorithm | Bowtie2 | (Langmead and Salzberg, 2012) PMID: 22388286 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| Software, algorithm | Samtools | (Li et al., 2009) PMID: 19505943 |
RRID:SCR_006646 | http://samtools.sourceforge.net/ |
| Software, algorithm | Bedtools | (Quinlan and Hall, 2010) PMID: 20110278 |
RRID:SCR_006646 | http://bedtools.readthedocs.io/en/latest/ |
| Software, algorithm | Deeptools | (Ramírez et al., 2016) PMID: 27079975 |
RRID:SCR_016366 | https://deeptools.readthedocs.io/en/develop/ |
| Software, algorithm | UCSC Genome Browser |
(Kent et al., 2002) PMID: 12045153 |
RRID:SCR_005780 | https://genome.ucsc.edu/ |
| Software, algorithm | PreprocessCore | (Bolstad, 2013) | https://www.bioconductor.org/packages/release/bioc/html/preprocessCore.html | |
| Software, algorithm | Biostrings | (Pagès et al., 2017) | https://bioconductor.org/packages/release/bioc/html/Biostrings.html | |
| Software, algorithm | EPIC | (Xu et al., 2014) PMID: 24743992 |
https://github.com/biocore-ntnu/epic | |
| Software, algorithm | Galaxy | (Afgan et al., 2016) PMID: 27137889 |
RRID:SCR_006281 | https://usegalaxy.org/ |
| Software, algorithm | ImageJ | (Schneider et al., 2012) PMID: 22930834 |
RRID:SCR_003070 | https://imagej.net/Welcome |
| Software, algorithm | Huygens Professional |
Huygens professional version 17.10 (Scientific volume imaging, The Netherlands) |
https://svi.nl/Huygens-Professional |