KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-V5 | Thermo Fisher Scientific | Cat#R960-25; RRID:AB_2556564 |
| Mouse monoclonal anti-Oct3/4 | Santa Cruz | Cat#sc-5279; RRID:AB_628051 |
| Chicken polyclonal anti-GFP | Abcam | Cat#ab13970; RRID:AB_300798 |
| Rabbit polyclonal anti-HA | Abcam | Cat#ab9110; RRID:AB_307019 |
| Rabbit polyclonal anti-H3K4me3 | Active Motif | Cat#39159; RRID:AB_2615077 |
| Rabbit polyclonal anti-H3K27me3 | Active Motif | Cat#39155; RRID:AB_2561020 |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat#ab4729; RRID:AB_2118291 |
| Rabbit polyclonal anti-V5 | Abcam | Cat#ab15828; RRID:AB_443253 |
| Rabbit polyclonal anti-mSIN3A | Abcam | Cat#ab3479; RRID:AB_303839 |
| Mouse monoclonal anti-CHD4 | Abcam | Cat#ab70469; RRID:AB_2229454 |
| Rabbit polyclonal anti-SETD1A | Abcam | Cat#ab70378; RRID:AB_1951955 |
| Rabbit polyclonal anti-NELF | Sigma | Cat#HPA007187; RRID:AB_1856161 |
| Rabbit polyclonal anti-POLS5P | Abcam | Cat#ab5131; RRID:AB_449369 |
| Goat polyclonal anti-SOX1 | R&D Systems | Cat#AF3369; RRID:AB_2239879 |
| Goat polyclonal anti-mouse | LI-COR Biosciences | Cat#925-32210; RRID:AB_2687825 |
| Goat polyclonal anti-mouse, Alexa Fluor 488 | Thermo Fisher Scientific | Cat#A-11029; RRID:AB_2534088 |
| Goat polyclonal anti-rabbit, Alexa Fluor 568 | Thermo Fisher Scientific | Cat#A-11036; RRID:AB_10563566 |
| Bacterial and virus strains | ||
| Endura Electro Competent Cells | Lucigen | Cat#60242 |
| 10-beta Competent E.Coli | NEB | Cat#C3019 |
| Chemicals, peptides, and recombinant proteins | ||
| CHIR 99021 | BioVision | Cat#1677-5; CAS:252917-06-9 |
| PD0325901 | Sigma | Cat#PZ0162; CAS:391210-10-9 |
| LIF | Millipore | Cat#ESG1107 |
| DSG | ProteoChem | Cat#c1104; CAS:79642-50-5 |
| Dynabeads protein-G | Thermo Fisher Scientific | Cat#10004D |
| Doxycycline | Sigma | Cat#D9891 |
| Lipofectamine 3000 Transfection Reagent | Thermo Scientific | Cat#100022052 |
| G418 | Sigma | Cat#1720; CAS: 108321-42-2 |
| Polybrene | EMD Millipore | Cat#TR1003G; CAS: 28728-55-4 |
| Zeocin | Invivogen | Cat#ant-zn-05; CAS: 11006-33-0 |
| PEI | Fisher Scientific | Cat# NC1014320; CAS: 9002-98-6 |
| Agencourt AmpureXP beads | Beckman Coulter | Cat#A63880 |
| Critical commercial assays | ||
| TruSeq Stranded mRNA Library Preparation kit | Illumina | Cat#20020594 |
| 10X Genomics Chromium Single Cell 3’ library kit | 10× Genomics | Cat#PN-120267 |
| Deposited data | ||
| Raw and analyzed sequencing data | This paper | GEO: GSE160966 |
| H3K4me1 ChIPseq data | (Creyghton et al., 2010) | GEO: GSE24165 |
| H3K9me3 ChIPseq data | (Bilodeau et al., 2009) | GEO: GSE18371 |
| OCT4, NANOG, and SOX2 ChIPseq data | (Marson et al., 2008) | GEO: GSE11724 |
| H3K4me2 ChIPseq data | (Meissner et al., 2008) | GEO: GSE11172 |
| ATAC-seq data | (Velasco et al., 2017) | GEO: GSE80511 |
| Experimental models: Cell lines | ||
| Mouse: A17 E14Tg2a | (Iacovino et al., 2011) | Wildtype |
| Mouse: iZbtb10-HA mESC line | This paper | iZbtb10-HA |
| Mouse: iZbtb11-HA mESC line | This paper | iZbtb11-HA |
| Mouse: iZfp131-HA mESC line | This paper | iZfp131-HA |
| Mouse: iZbtb10-HA Zbtb10Δ mESC line | This paper | iZbtb10-HA Zbtb10Δ |
| Mouse: iZbtb11-HA Zbtb11Δ mESC line | This paper | iZbtb11-HA Zbtb11Δ |
| Mouse: iZfp131-HA Zfp131Δ mESC line | This paper | iZfp131-HA Zfp131Δ |
| Mouse: iZbtb11-HA iZfp131-V5 Zbtb11Δ mESC line | This paper | iZbtb11-HA iZfp131-V5 Zbtb11Δ |
| Mouse: iZbtb11-HA iZfp131-V5 Zbtb11Δ Zfp131Δ mESC line | This paper | iZbtb11-HA iZfp131-V5 Zbtb11Δ Zfp131Δ |
| Mouse: Oct4::tdTomato Sox2::Gfp mESC line | This paper | Oct4::tdTomato Sox2::Gfp |
| Mouse: H2B-GFP mESC line | This paper | H2B-GFP |
| Human: HEK 293T cells | ATCC | Cat# CRL-3216, RRID:CVCL_0063 |
| Human: NYGCe001-A hESC line | (Lu and Sanjana, 2019) | RRID:CVCL_YC46 |
| Oligonucleotides | ||
| See Table S3 for all oligonucleotides | This paper | N/A |
| Recombinant DNA | ||
| See Table S3 for all plasmids | This paper | N/A |
| Software and algorithms | ||
| Hisat2 (version 2.1.0) | (Kim et al., 2015) | http://daehwankimlab.github.io/hisat2/ |
| featureCounts (version 1.22.2) | (Liao et al., 2014) | https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts |
| DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| PANTHER (version 16) | (Mi et al., 2019) | http://geneontology.org |
| 10X Genomics CellRanger (version 4.0.0) | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Seurat R package (version 3.0) | (Stuart et al., 2019) | https://satijalab.org/seurat/ |
| MultiGPS (version 0.74) | (Mahony et al., 2014) | https://mahonylab.org/software/multigps/ |
| Bowtie (version 1.0.1) | (Langmead et al., 2009) | http://bowtie-bio.sourceforge.net/index.shtml |
| RepeatMasker (version 4.0.7) | (Smit et al., 1996) | https://www.repeatmasker.org/ |
| MEME suite (version 4.11.3) | (Bailey et al., 2015) | https://meme-suite.org/meme/doc/download.html |
| Deeptools (version 3.1.3) | (Ramírez et al., 2016) | https://deeptools.readthedocs.io/en/develop/ |