Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens) | Raji (lymphoblast) | ATCC/DZMZ | ATCC: CCL-86 DZMZ: ACC 319 RRID:CVCL_0511 |
B-lymphocyte; Burkitt’slymphoma Received from:https://www.dsmz.de/collection/catalogue/details/culture/AC C-319 Tested mycoplasma negative |
| Antibody | Cyclin A1/A2 (rabbit monoclonal) | Abcam | ab185619 | WB: 1:1000 |
| Antibody | Cyclin B1 (mouse monoclonal) | Abcam | ab72, RRID:AB_305751 |
WB: 1:1000 |
| Antibody | H3S10P (rabbit monoclonal) | Cell Signaling | Clone D2C8, cat. no. 3377, RRID:AB_1549592 |
WB: 1:1000 |
| Antibody | GAPDH (rat monoclonal) | This paper | Clone GAPDH3 10F4; Rat IgG2c |
WB: 1:50 |
| Antibody | H4K20me1 (mouse monoclonal) | Diagenode | MAb-147-100 | ChIP: 2.5 µg |
| Antibody | H4K20me3 (rabbit polyclonal) | Diagenode | pAb-057-050, RRID:AB_2617145 |
ChIP: 2.5 µg |
| Antibody | Rabbit-IgG (polyclonal) | Sigma | R2004, RRID:AB_261311 |
ChIP: 10 µg |
| Antibody | Orc2 (rabbit polyclonal) |
Ritzi et al., 2003 | SA93 | Whole serum; ChIP: 15 µl |
| Antibody | Orc3 (rabbit polyclonal) |
Ritzi et al., 2003 | SA7976 | Whole serum; ChIP: 15 µl |
| Antibody | Mcm3 (rabbit polyclonal) |
Ritzi et al., 2003 | SA8413 | Whole serum; ChIP: 15 µl |
| Antibody | Mcm7 (rabbit polyclonal) |
Ritzi et al., 2003 | SA8496 | Whole serum; ChIP: 15 µl |
| Peptide, recombinant protein | Protein A Sepharose 4 Fast Flow | GE Healthcare | GE17-5280-11 | |
| Peptide, recombinant protein | Protein G Sepharose 4 Fast Flow | GE Healthcare | GE17-0618-06 | |
| Sequence-based reagent | oriP DS_fw | This paper | qPCR primers | 5′-AGTTCACTGCCCGCTCCT-3′ |
| Sequence-based reagent | oriP DS_rv | This paper | qPCR primers | 5′-CAGGATTCCACGAGGGTAGT-3′ |
| Sequence-based reagent | H4K20me1positive_fw | Eric Julien, personal communication | qPCR primers | 5′-ATGCCTTCTTGCCTCTTGTC-3′ |
| Sequence-based reagent | H4K20me1positive_rv | Eric Julien, personal communication | qPCR primers | 5′-AGTTAAAAGCAGCCCTGGTG-3′ |
| Sequence-based reagent | H4K20me3positive_fw | Eric Julien, personal communication | qPCR primers | 5′-TCTGAGCAGGGTTGCAAGTAC-3′ |
| Sequence-based reagent | H4K20me3positive_rv | Eric Julien, personal communication | qPCR primers | 5′-AAGGAAATGATGCCCAGCTG-3′ |
| Chemical compound, drug | Formaldehyde | Thermo Scientific | Prod# 28908 | 16% formaldehyde solution; methanol-free |
| Chemical compound, drug | Proteinase K | Roche | Cat. no. 03 115 852 001 | 1 mg/ml; 8 mg |
| Chemical compound, drug | RNase | Roche | Cat. no. 11 119 915 001 | 0.5 µg/µl; 2 µg |
| Commercial assay or kit | NucleoSpin Extract II Kit | Macherey-Nagel | Cat. no. 740609.50 | |
| Commercial assay or kit | Accel-NGS 1S Plus DNA Library Kit for Illumina | Swift Biosciences | Cat. no. 10096 | |
| Commercial assay or kit | Direct-zolTM RNA MiniPrep kit | Zymo Research | Cat. no. R2051 | |
| Commercial assay or kit | Encore Complete RNA-Seq Library Systems kit | NuGEN | Cat. no. 0333-32 |
|
| Software, algorithm | Tophat2 | Kim et al., 2013 | RRID:SCR_013035 | |
| Software, algorithm | HTSeq-count | Anders et al., 2015 | RRID:SCR_011867 | |
| Software, algorithm | BWA (v.0.7.4) | Li and Durbin, 2009 | RRID:SCR_010910 | OK-seq mapping, default parameters |
| Software, algorithm | bowtie (v.1.1.1) | Langmead et al., 2009 | RRID:SCR_005476 | ChIP-seq mapping, bowtie -m one index file.fastq |
| Software, algorithm | deepTools (v.3.3.1) | Ramírez et al., 2016 | RRID:SCR_016366 | |
| Software, algorithm | MACS2 (v.2.2.5) | Zhang et al., 2008 | RRID:SCR_013291 | Default settings, --broad |
| Software, algorithm | R (v.3.2.3) | R Development Core Team, 2018 | RRID:SCR_001905 | |
| Software, algorithm | dplyr (v.0.8.5) | Wickham et al., 2020 | RRID:SCR_016708 | R package |
| Software, algorithm | ggplot2 (v.3.1.0) | Wickham, 2016 | RRID:SCR_014601 | R package |
| Software, algorithm | gplots (v.3.0.3) | Warnes et al., 2020 | R package | |
| Software, algorithm | Python 2.7 and Phyton 3 | van Rossum, 1995 | RRID:SCR_008394 | |
| Software, algorithm | numpy (v.1.18.5) | Harris et al., 2020 | RRID:SCR_008633 | Python library |
| Software, algorithm | matplotlib (v.3.2.3) | Hunter, 2007 | RRID:SCR_008624 | Python library |
| Software, algorithm | SciPy (v.1.5.0) | Virtanen et al., 2020 | RRID:SCR_008058 | Python library |