KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-MOF | Bethyl Laboratories | Cat#A300-992A; RRID:AB_805802 |
| Anti-OCT3/4 | Santa Cruz Biotechnology | Cat#sc-5279; RRID:AB_628051 |
| Anti-NANOG | Novus Biologicals | Cat#AF2729; RRID:AB_2150103 |
| Anti-OTX2 | R & D Systems | Cat#AF1979; RRID:AB_2157172 |
| Anti-SMA | SIGMA ALDRICH | Cat#A2547; RRID:AB_476701 |
| Anti-TUJ1 | Biolegend | Cat#801201; RRID:AB_2313773 |
| Anti-SOX17 | R & D Systems | Cat#AF1924; RRID:AB_355060 |
| Anti-KLF4 | Santa Cruz Biotechnology | Cat#sc-166238; RRID:AB_2130234 |
| Anti-TFCP2L1 | R & D Systems | Cat#AF5726; RRID:AB_2202564 |
| Anti-β-ACTIN | Santa Cruz Biotechnology | Cat#sc47778; RRID:AB_2714189 |
| Anti-AMPKα | Cell signaling | Cat#2532; RRID:AB_330331 |
| Anti-Phospho-AMPKα (Thr172) | Cell signaling | Cat#4188; RRID:AB_2169396 |
| Anti-S6K1 | Santa Cruz Biotechnology | Cat#sc-230; RRID:AB_632156 |
| Anti-Phospho-S6K1 (Thr389) | Cell signaling | Cat#9234; RRID:AB_2269803 |
| Anti-AKT | Cell signaling | Cat#9272; RRID:AB_329827 |
| Anti-Phospho-AKT (Ser473) | Cell signaling | Cat#4060; RRID:AB_2315049 |
| Anti-H4K16ac | Millipore | Cat#07-329; RRID:AB_310525 |
| Anti-H3K27ac | Abcam | Cat#ab4729; RRID:AB_2118291 |
| Anti-H3K9ac | Abcam | Cat#ab4441; RRID:AB_2118292 |
| Anti-H3K56ac | Abcam | Cat#ab76307; RRID:AB_1523762 |
| Anti-H4ac | Millipore | Cat# 06-866; RRID:AB_310270 |
| Anti-Histone H3 | Abcam | Cat#ab1791; RRID:AB_302613 |
| Anti-Histone H4 | Active Motif | Cat#39269; RRID:AB_2636967 |
| Goat anti-Mouse IgG Alexa FluorR 555 | Abcam | Cat#ab150114; RRID:AB_2687594 |
| Goat anti-Rabbit IgG Alexa Fluor Plus 647 | Thermo Fisher Scientific | Cat#A32733; RRID:AB_2633282 |
| Goat anti-Mouse IgG FITC-conjugated | Thermo Fisher Scientific | Cat#62-6511; RRID:AB_2533946 |
| Donkey anti-Mouse Alexa Fluor 647 | Thermo Fisher Scientific | Cat#A-31571; RRID:AB_162542 |
| Donkey anti-Goat IgG AlexaFluorR 555 | Abcam | Cat#ab150130; RRID:AB_10894526 |
| Donkey anti-Goat IgG AlexaFluor 488 | Thermo Fisher Scientific | Cat#A-11055; RRID:AB_2534102 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| ESGRO® leukemia inhibitory factor (LIF) | EMD Millipore | Cat#ESG1107 |
| human LIF | SIGMA ALDRICH | Cat#L5283 |
| PD0325901 | SIGMA ALDRICH | Cat#PZ0162 |
| CHIR99021 | SIGMA ALDRICH | Cat#SML1046 |
| Geltrex | Thermo Fisher Scientific | Cat#A1413202 Cat#A1413302 |
| Ndiff227 media | Clontech | Cat#Y40002 |
| Activin A | R & D Systems | Cat#338-AC |
| bFGF | R & D Systems | Cat#233-FB |
| N2 supplement 100X | Thermo Fisher Scientific | Cat#17502001 |
| B27 supplement 50X | Thermo Fisher Scientific | Cat#17504-044 |
| mTeSR1 media | STEMCELL Technologies | Cat#85850 |
| Gö6983 | SIGMA ALDRICH | Cat#G1918 |
| L-Carnitine | SIGMA ALDRICH | Cat#C0158 |
| O-Acetyl-L-Carnitine | SIGMA ALDRICH | Cat#A6706 |
| AICAR | Cayman | Cat#10010241 |
| Coenzyme A | SIGMA ALDRICH | Cat#C4780 |
| Etomoxir | SIGMA ALDRICH | Cat#E1905 |
| Trimetazidine | SIGMA ALDRICH | Cat#653322 |
| INK128 | Medchem Express | Cat#HY-13328 |
| Oligomycin A | Cayman | Cat#11342 |
| FCCP | Cayman | Cat#15218 |
| Antimycin A | SIGMA ALDRICH | Cat#A8674 |
| Rotenone | SIGMA ALDRICH | Cat#R8875 |
| KSOMaa EvolveR medium | Zenith Biotech | Cat#ZEKS-050 |
| Bovine Serum Albumin solution | SIGMA ALDRICH | Cat#A8412 |
| MitoTracker Red CMXRos | SIGMA ALDRICH | Cat#M7512 |
| Tetramethylrhodamine methyl ester | Thermo Fisher Scientific | Cat#T668 |
| Hoechst 33342 | Thermo Fisher Scientific | Cat#62249 |
| Pyronin Y | SIGMA ALDRICH | Cat#213519 |
| Propidium Iodide | SIGMA ALDRICH | Cat#00-6990-50 |
| FITC-Annexin V | Bioscience | Cat#556419 |
| O-Propargyl Puromycin (OP-Puro) | Jena Bioscience | Cat#NU-931-05 |
| Critical Commercial Assays | ||
| VECTOR® Red Alkaline Phosphatase Kit | Vector Laboratories | Cat#SK-5100 |
| LookOut® Mycoplasma PCR Detection Kit | SIGMA ALDRICH | Cat#MP0035 |
| Click-iT™ Plus EdU Flow Cytometry Assay Kits | Thermo Fisher Scientific | Cat#C10632 Cat#C10634 |
| Click-iT Cell Reaction Buffer Kit | Thermo Fisher Scientific | Cat#C10269 |
| Qubit™ RNA HS assay kit | Thermo Fisher Scientific | Cat#Q32855 |
| Seahorse XF Base Medium | Agilent Technologies | Cat#102353-100 |
| Deposited Data | ||
| RNA-seq | This paper | GSE137138 |
| Experimental Models: Cell Lines | ||
| Mouse ES cells: E14tg2a | ATCC | Cat#CRL-1821™ |
| Mouse ES cells: Moffl/fl; Cre-ER™ | Y. Dou | Li et al., 2012 |
| Mouse ES cells: Oct4-GiP | Austin Smith | Ying et al., 2008 |
| MEFs | This paper | N/A |
| Human ES cells: Primed H9 | WiCell | Cat#WAe009-A |
| Human ES cells: Naive H9 | Austin Smith | Guo et al., 2017 Takashima et al., 2014 |
| Experimental Models: Organisms/Strains | ||
| (C57BL/6J × DBA/2J)F1 females | Jackson Laboratory | Cat#100006 |
| (C57BL/6J × DBA/2J)F1 males | Jackson Laboratory | Cat#100006 |
| C57BL/6NCrl female | Charles River Laboratory | Cat#493 |
| (C57BL/6J × SJL/J)F1 males | Jackson Laboratory | Cat#100012 |
| Oligonucleotides | ||
| Primers for RT-qPCR (see Table S7) | This paper | N/A |
| Software and Algorithms | ||
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| Tophat2, v2.1.1 | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/manual.shtml |
| Integrative Genomics Viewer (IGV), v2.3 | Thorvaldsdóttir et al., 2013 | http://software.broadinstitute.org/software/igv/ |
| Cufflinks, v2.2.1 | Trapnell et al., 2012 | http://cole-trapnell-lab.github.io/cuffiinks/ |
| CummeRbund, v2.1 | N/A | http://compbio.mit.edu/cummeRbund/ |
| Bowtie2, v2-2.2.4 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MACS, v1.4 | Zhang et al., 2008 | http://liulab.dfci.harvard.edu/MACS/ |
| HOMER v4.10 | Salk Institute | http://homer.ucsd.edu/homer/ |
| DeepTools, v3.2.1 | Ramírez et al., 2016 | https://github.com/deeptools/deepTools |
| Panther Classification System, v13.0 | N/A | http://pantherdb.org/ |
| Mouse ENCODE Consortium | Amemiya et al., 2019; ENCODE Project Consortium et al., 2012 | https://sites.google.com/site/anshulkundaje/projects/blacklists |
| GraphPad Prism, v7 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo, v10.0.7r2 | FlowJo LLC | https://docs.fiowjo.com:443 |
| bcl2fastq2 software (v2.17) | Illumina LLC | https://support.illumina.com/sequencing/conversion-software.html |
| Cutadapt | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
| FastQC | Babraham institute | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Trim Galore | Babraham institute | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| EpiProfileLite | Sidoli et al., 2019 | https://github.com/zfyuan/EpiProfileLite |
| MetaboAnalyst 4.0 | Chong et al., 2018 | https://www.metaboanalyst.ca |
| Agilent MassHunter Quantitative Analysis (for QQQ) Version B.07 | Agilent Technologies | https://www.agilent.com/en/support/software-informatics/qual-b-0700-sp1 |
| Other | ||
| RNA-seq for early embryonic stages | Boroviak et al., 2015 | E-MTAB-2958 |
| RNA-seq for dormant state by Myc deletion | Scognamiglio et al., 2016 | E-MTAB-3386 |
| RNA-seq for paused state by mTOR inhibition | Bulut-Karslioglu et al., 2016 | GSE81285 |
| ChIP-seq for MOF | Li et al., 2012 | GSE37268 |
| ChIP-seq for H4K16ac | Valsecchi et al., 2018 | GSE109897 |
| ChIP-seq for H4K16ac | Taylor et al., 2013 | GSE47761 |