Gene (H. sapiens) | ATRX | NA | NCBI Gene ID: 546 | |
Strain, strain background (Herpes simplex virus 1) | KOS | Smith, 1964 | | |
Strain, strain background (Herpes simplex virus 1) | HSV-EdC | This Paper | | From HSV KOS |
Strain, strain background (Herpes simplex virus 1) | HSV 7134 | Cai and Schaffer, 1992, PMID: 1313909 | | |
Strain, strain background (Herpes simplex virus 1) | HSV 7134R | Cai and Schaffer, 1992, PMID: 1313910 | | |
Strain, strain background (Herpes simplex virus 1) | HSV d109 | Samaniego et al., 1998; PMID: 9525658 | | |
Cell line (H. sapiens) | Human Foreskin Fibroblast (HFF) | American Type Culture Collection | SCRC-1041 | |
Cell line (H. sapiens) | TERT-HF | Bresnahan and Shenk, 2000, PMID: 10875924 | | via Robert Kalejta |
Cell line (H. sapiens) | TERT-HF Control | This paper | | |
Cell line (H. sapiens) | TERT-HF ATRX-KO | This paper | | |
Cell line (H. sapiens) | 293T | American Type Culture Collection | CRL-3216 | |
Cell line (H. sapiens) | shControl | Wagenknecht et al., 2015, PMID: 26057166 | | |
Cell line (H. sapiens) | shPML | Wagenknecht et al., 2015, PMID: 26057166 | | |
Cell line (H. sapiens) | U2OS | American Type Culture Collection | HTB-96 | |
Antibody | Anti-ATRX, rabbit polyclonal | Abcam | ab97508 | 1:500 IF; 1:2000 WB; 6 µg/ChIP rxn |
Antibody | Anti-IFI16 [IFI-230], mouse monoclonal | Abcam | ab50004 | 1:2500 WB;1:500 IF |
Antibody | Anti-PML, rabbit polyclonal | Bethyl | A301-167A | 1:2000 WB |
Antibody | Anti-DAXX, rabbit polyclonal | Sigma | D7810 | 1:2000 WB |
Antibody | Anti-ICP4 (58S), mouse monoclonal | Showalter et al., 1981, PMID: 6277788 | | 1:2000 WB; 1:500 IF |
Antibody | Anti-ICP8 (383), rabbit polyclonal | Knipe et al., 1987, PMID: 3027360 | | 1:2000 WB; 1:500 IF |
Antibody | anti-GAPDH [EPR16891], rabbit monoclonal | Abcam | ab181602 | 1:5000 WB |
Antibody | anti- HSV 1-ICP0, mouse monoclonal | East Coast Bio | H1A207 | 1:5000–10000 IF |
Antibody | Anti-PML [C7], mouse monoclonal | Abcam | ab96051 | 1:500 IF |
Antibody | Anti- Histone H3 ChIP Grade, rabbit polyclonal | Abcam | ab1791 | 2.5 µg/ChIP rxn |
Antibody | Anti-Histone H3.3, rabbit polyclonal | Millipore | 09–838 | 2.5 µg/ChIP rxn |
Antibody | Anti-H3K9me3 ChIP Grade, rabbit polyclonal | Abcam | ab8898 | 2.5 µg/ChIP rxn |
Antibody | Anti-Histone H3K27me3, rabbit polyclonal | Active Motif | 39156 | 2.5 µg/ChIP rxn |
Antibody | Normal Rabbit IgG, rabbit polyclonal | Millipore | NG1893918 | 2.5 µg/ChIP rxn (6 µg/ATRX ChIP) |
Recombinant DNA reagent | lentiCRISPR v2 | Addgene | Plasmid #52961 | |
Sequence-based reagent | ICP8 cDNA FWD | IDT | | 5'-GTCGTTACCGAGGGCTTCAA |
Sequence-based reagent | ICP8 cDNA REV | IDT | | 5'-GTTACCTTGTCCGAGCCTCC |
Sequence-based reagent | ICP27 cDNA FWD | IDT | | 5'-GCATCCTTCGTGTTTGTCATT |
Sequence-based reagent | ICP27 cDNA REV | IDT | | 5'-GCATCTTCTCTCCGACCCCG |
Sequence-based reagent | gB cDNA FWD | IDT | | 5'-TGTGTACATGTCCCCGTTTTACG |
Sequence-based reagent | gB cDNA REV | IDT | | 5'-GCGTAGAAGCCGTCAACCT |
Sequence-based reagent | ICP4 cDNA FWD | IDT | | 5'-GCGTCGTCGAGGTCGT |
Sequence-based reagent | ICP4 cDNA REV | IDT | | 5'-CGCGGAGACGGAGGAG |
Sequence-based reagent | Q-RT 18 S F | IDT | | 5'-GCCGCTAGAGGTGAAATTCTTG |
Sequence-based reagent | Q-RT 18 S R | IDT | | 5'-CTTTCGCTCTGGTCCGTCTT |
Sequence-based reagent | ICP27 Promoter FWD (ChIP) | IDT | | 5'-ACCCAGCCAGCGTATCCACC |
Sequence-based reagent | ICP27 Promoter REV (ChIP) | IDT | | 5'-ACACCATAAGTACGTGGC |
Sequence-based reagent | ICP8 Promoter FWD (ChIP) | IDT | | 5'-GAGACCGGGGTTGGGGAATGAATC |
Sequence-based reagent | ICP8 Promoter REV (ChIP) | IDT | | 5'-CCCCGGGGGTTGTCTGTGAAGG |
Sequence-based reagent | GAPDH Promoter FWD (ChIP) | IDT | | 5'-CAGGCGCCCAATACGACCAAAATC |
Sequence-based reagent | GAPDH Promoter REV (ChIP) | IDT | | 5'-TTCGACAGTCAGTCAGCCGCATCTTCTT |
Sequence-based reagent | sgATRX 1 F | This paper | | 5'-TCTACGCAACCTTGGTCGAA |
Sequence-based reagent | sgATRX 1 R | This paper | | 5'-TTCGACCAAGGTTGCGTAGA |
Sequence-based reagent | sgATRX 2 F | This paper | | 5'-CGAAACTAACAGCTGAACCC |
Sequence-based reagent | sgATRX 2 R | This paper | | 5'-GGGTTCAGCTGTTAGTTTCG |
Sequence-based reagent | siNT | Dharmacon | ON-TARGETplus Non-targeting pool D-001810–10 | |
Sequence-based reagent | siATRX | Dharmacon | ON-TARGETplus ATRX pool D-006524–00 | |
Sequence-based reagent | siIFI16 | Dharmacon | ON-TARGETplus IFI16 pool D-20004–00 | |
Sequence-based reagent | siDAXX | Dharmacon | ON-TARGETplus DAXX pool D-004420–10 | |
Peptide, recombinant protein | Streptavidin-488 | Invitrogen | 532354 | 1:1000 |
Peptide, recombinant protein | RNase A | Thermo Science | EN0531 | |
Commercial assay or kit | DNase Free Kit | Invitrogen | AM1906 | |
Commercial assay or kit | RNeasy Kit | Qiagen | 74106 | |
Commercial assay or kit | QIAquick PCR Purification Kit | Qiagen | 28106 | |
Commercial assay or kit | High Capacity CDNA Kit | Applied BioSys | 4368814 | |
Software, algorithm | Foci-detection and colocalization software | This paper - Image and Data Analysis Core (IDAC) at Harvard Medical School; doi: 10.5061/dryad.95fs76f | | MATLAB based package; https://datadryad.org/resource/doi:10.5061/dryad.95fs76f |
Chemical compound, drug | Picolyl-biotin azide | Click Chemistry Tools | product# 1167 | 10 µM final conc. |
Chemical compound, drug | sodium ascorbate | Sigma | #a4034 | |
Chemical compound, drug | CuSO4 | Fisher | C489 | |
Chemical compound, drug | EdC | Sigma | T511307 | 25 mM stock |
Chemical compound, drug | Prolong gold | Invitrogen | P36934 | |
Chemical compound, drug | EM Formaldehyde (IF) | Thermo Science | 2908 | 16% methanol free - 2% working conc. |
Chemical compound, drug | Formaldehyde (ChIP) | Sigma | F8775 | 1% for ChIP crosslinking |
Chemical compound, drug | Actinomycin-D | Sigma | A1410 | 5 µg/mL final |
Chemical compound, drug | α-Amanitin | Sigma | A2263 | 2 µg/mL final |
Chemical compound, drug | Phosphono Acetate | Sigma | 284270 | 400 µg/mL final |
Chemical compound, drug | Puromycin | Santa Cruz | CAS 53-79-2 | 5 µg/mL final |
Chemical compound, drug | Roche Complete protease inhibitor | Sigma-Aldrich | 11697498001 | |
Chemical compound, drug | Fast-Sybr sybr green (qPCR) | Applied Biosystems | 4385612 | |
Chemical compound, drug | Lipofectamine RNAiMAX transfection reagent | Invitrogen | 56532 | |