KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal Histone H3 (phospho S10) | Abcam | Cat# ab47297 |
| Rabbit polyclonal to Histone H3 (acetyl K27) | Abcam | Cat# ab4729 |
| Rabbit polyclonal to Histone H3 | Abcam | Cat# ab1791 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Nocodazole | Sigma | Cat# M1404 |
| MEK inhibitor (PD0325901) | Stemgent | Cat# 04-0006 |
| GSK inhibitor (CHIR99021) | Stemgent | Cat# 04-0004-10 |
| A 485 (p300/CBP inhibitor) | Tocris | Cat# 6387 |
| Critical Commercial Assays | ||
| Nextera DNA library Preparation Kit | Illumina | Cat# FC-121-103 |
| SeqCap Adapter Kit A | Roche | Cat# 7141530001 |
| KAPA HiFi HotStart ReadyMix and primers | KAPA | Cat# KK2620 |
| KAPA Hyper Prep Kit | KAPA | Cat# KK8502 |
| Arima-HiC Kit | Arima | Cat# A510008 |
| Deposited Data | ||
| Raw and processed data of ATAC-seq libraries in mitotic and asynchronous mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of Hi-C libraries for mitotic release time course in mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of PRO-seq libraries for mitotic release time course in mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of 4C-seq libraries at 11 loci for mitotic release time course in mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of RNA-seq libraries in asynchronous mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of H3K27ac ChIP-seq libraries after DMSO or p300i (A485) treatment in mitosis, early G1, and asynchronous mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of PRO-seq libraries after DMSO or p300i (A485) treatment in mitosis, early G1, and asynchronous mouse PSCs |
This study | GEO: GSE138965 |
| Raw and processed data of Hi-C libraries after DMSO or p300i (A485) treatment in mitosis, early G1, and asynchronous mouse PSCs |
This study | GEO: GSE138965 |
| H3K27ac and KLF4 ChIP-seq in mitotic and asynchronous mouse embryonic stem cells |
Liu et al., 2017b | GEO: GSE92846 |
| TBP ChIP-seq in mitotic and asynchronous mouse embryonic stem cells |
Teves et al., 2018 | GEO: GSE109962 |
| ESRRB ChIP-seq in mitotic and asynchronous mouse embryonic stem cells |
Festuccia et al., 2016 | GEO: GSE75066 |
| CTCF ChIP-seq in mitotic and asynchronous mouse embryonic stem cells |
Owens et al., 2019 | GEO: GSE131356 |
| OCT4 and NANOG ChIP-seq in mitotic and asynchronous mouse embryonic stem cells |
Festuccia et al., 2019 | GEO: GSE122589 |
| H3K27ac Hi-ChIP in asynchronous mouse embryonic stem cells |
Di Giammartino et al., 2019 | GEO: GSE113431 |
| Micro-C in mouse embryonic stem cells: valid pairs and .hic matrix files |
Hsieh et al., 2020 | GEO: GSE130275 |
| Drosophila reference genome (Dm6) | Berkeley Drosophila Genome Project |
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/ |
| Mouse reference genome GRCm38 (mm10) | Genome Reference Consortium |
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ |
| Experimental Models: Cell Lines | ||
| FUCCI2a iPSC clone A | This study | N/A |
| FUCCI2a iPSC clone B | This study | N/A |
| Oligonucleotides | ||
| See Table S5 for all oligonucleotide sequences | This study Krijger et al., 2020 |
N/A |
| Software and Algorithms | ||
| FlowJo (v10.6.1) | FlowJo | http://docs.flowjo.com/d2/ |
| FIJI (ImageJ v2.0.0) | Schindelin et al., 2012 | https://imagej.net/Fiji |
| Bowtie 2 aligner (v2.2.6) | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Tophat2 (v2.1.0) | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| Picard (MarkDuplicates command, v2.12.2) | Broad Institute | https://broadinstitute.github.io/picard/ |
| Samtools (v1.7) | Li et al., 2009 | http://samtools.sourceforge.net/ |
| MACS2 (v2.1.1) | Zhang et al., 2008 | https://pypi.org/project/MACS2/#description |
| IGV browser | Robinson et al., 2011 | https://software.broadinstitute.org/software/igv/ |
| Bedtools (v2.25.0) | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Htseq-count (0.5.4.p3) | Anders et al., 2015 | https://htseq.readthedocs.io/en/release_0.11.1/history.html#version-0-5-4 |
| DeepTools (version 3.0.2) | Ramirez et al, 2016 | https://deeptools.readthedocs.io/en/develop/index.html# |
| Fastx-toolkit (0.0.13) | FastX-Toolkit | http://hannonlab.cshl.edu/fastx_toolkit/ |
| Cutadapt (v1.4.2) | Martin, 2011 | https://doi.org/10.14806/ej.17.1.200 |
| dREG | Danko et al., 2015; Wang et al., 2019 | https://github.com/Danko-Lab/dREG |
| HiCexplorer (v1.8) | Ramirez et al., 2018 | https://hicexplorer.readthedocs.io/en/latest/ |
| FitHiC (1.1.3) | Ay et al., 2014 | https://noble.gs.washington.edu/proj/fit-hi-c/ |
| R (3.4.4) | R Core Team, 2020 | https://www.R-project.org/ |
| LOLA (v1.0.0) | Sheffield and Bock, 2016 | http://code.databio.org/LOLA/ |
| DESeq | Anders and Huber, 2010 | https://bioconductor.org/packages/release/bioc/html/DESeq.html |
| Cscore algorithm (v1.1) | Zheng and Zheng, 2018 | https://github.com/scoutzxb/CscoreTool |
| David knowledgebase (v6.8) | Dennis et al., 2003 | https://david.ncifcrf.gov/ |
| GREAT analysis (v3.0.0) | McLean et al., 2010 | http://great.stanford.edu/great/public-3.0.0/html/ |
| Juicebox | Robinson et al., 2018 | https://www.aidenlab.org/juicebox/ |
| Juicer tools (v1.19.02) | Durand et al., 2016 | https://github.com/aidenlab/juicer |