KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Rinf | Cell signaling Technology | Cat# 84546; RRID:AB_2800040 |
| Anti-V5 | Cell signaling Technology | Cat# 13202; RRID:AB_2687461 |
| Anti-Flag | Cell signaling Technology | Cat# 14793; RRID:AB_2572291 |
| Anti-Tet1 | GenTex | Cat# GTX125888; RRID:AB_11164485 |
| Anti-Tet2 | Abcam | Cat# ab124297; RRID:AB_2722695 |
| Anti-Nanog | Bethyl Laboratories | Cat# A300-397A; RRID:AB_386108 |
| Anti-Oct4 | SantaCruz | Cat# SC-5279; RRID:AB_628051 |
| Anti-H3 | Abcam | Cat# ab1791; RRID:AB_302613 |
| Anti-Actin | Abcam | Cat# ab82618; RRID:AB_1658432 |
| Anti-Nestin | R&D | Cat# MAB533; RRID:AB_2070659 |
| Anti-Sox2 | EMD Millipore Corp. | Cat# AB5603; RRID:AB_2286686 |
| Anti-E-cadherin | BD Biosciences | Cat# 610182; RRID:AB_397581 |
| Anti-Dnmt3a | Novus Biologicals | Cat# NB120-13888; RRID:AB_789607 |
| Anti-Dnmt3b | Santa Cruz | Cat# SC-376043; RRID:AB_10988201 |
| Anti-5hmC | Active Motif | Cat# 39769; RRID:AB_10013602 |
| Anti-5mC | Cell Signaling Technology | Cat# 28692; RRID:AB_2798962 |
| Goat Anti-Rabbit IgG-HRP | Millipore | Cat# 401393-2ML; RRID:AB_10683386 |
| Goat Anti-Mouse IgG-HRP | Millipore | Cat# 401253; RRID:AB_437779 |
| Alexa Flour 488 -anti-rabbit | Life Technologies | Cat# A-21206; RRID:AB_2535792 |
| Alexa Flour 594 -anti-mouse | Life Technologies | Cat# A-11005; RRID:AB_2534073 |
| Critical Commercial Assays | ||
| Dual Luciferase reporter assay kit | Promega | E1910 |
| E.Z.N.A. Total RNA kit | Omega | R6834-02 |
| Superscript III first strand | Invitrogen | 18080-400 |
| Qubit dsDNA HS assay kit | Invitrogen | Q32851 |
| Xfect mESC polymer | Clonetech | 631320 |
| XtremeGene 9 DNA transfection reagent | Roche | 06365787001 |
| TNT Coupled transcription and translation kit | Promega | L1170 |
| Deposited Data | ||
| ChIP-seq data | This paper | GEO: GSE132025 |
| RNA-seq data | This paper | GEO: GSE132025 |
| Experimental Models: Cell Lines | ||
| Rinf−/− ESC | This paper | N/A |
| RinfV5/V5 ESC | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| SCID mice | Taconic | Model#ICRSC-M |
| Oligonucleotides | ||
| RT-qPCR primers, see Table S1 | This paper | N/A |
| ChIP-qPCR Primers, see Tables S1 and S2 | This paper | N/A |
| Genotyping Primers, see Table S1 | This paper | N/A |
| gRNA oligos for gene targeting, see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| PiggyBac-hygro | This paper | N/A |
| PiggyBac-V5-mRinf-hygro | This paper | N/A |
| PiggyBac-mTet1-CD-hygro | This paper | N/A |
| PiggyBac-mTet2-hygro | This paper | N/A |
| FUW-Nanog | This paper | N/A |
| FUW-Oct4 | This paper | N/A |
| pGL4.23-empty vector | Promega | E8411 |
| pGL4.75-empty vector | Promega | E6931 |
| pGL4.23-Tet1 Enhancer | This paper | N/A |
| pGL4.23-Nanog Enhancer | This paper | N/A |
| pGL4.23-Sox2 Enhancer | This paper | N/A |
| pRUTH5-mRinf | This paper | N/A |
| pRUTH5-mNanog | This paper | N/A |
| pRUTH5-mTet2-CD (aa1040-1910) | This paper | N/A |
| Software and Algorithms | ||
| Trim galore v0.4.1 | Github | https://github.com/FelixKrueger/TrimGalore |
| MACS2 v2.1.0 | Zhang et al., 2008 | https://github.com/taoliu/MACS/ |
| seqMINER v1.2.1 | Ye etal., 2011 | http://bips.u-strasbg.fr/ |
| HOMER v4.7 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Bowtie v2.2.3 | John Hopkins University | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Tophat v2.0.13 | John Hopkins University | https://ccb.jhu.edu/software/tophat/index.shtml |
| HTSeq v0.6.1 | Anders et al., 2015 | https://github.com/simon-anders/htseq |
| Cufflinks v2.2 | Trapnell et al., 2010 | http://cole-trapnell-lab.github.io/cufflinks/ |
| DESeq2 v1.20.0 | Love et al., 2014 | http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Integrative Genomics Viewer (IGV) v2.5.0 | Broad Institute | http://software.broadinstitute.org/software/igv/ |
| DAVID 6.8 | Jiao et al., 2012 | https://david.ncifcrf.gov/ |
| GraphPad Prism 7 | GraphPad | https://www.graphpad.com/ |
| ImageJ | Schneider et al., 2012 | https://imagei.nih.gov/ii/ |