KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-H3K4me1 | Abcam | Cat# ab8895; RRID: AB_306847 |
| anti-H3K4me2 | Millipore | Cat# 07–030; RRID: AB_310342 |
| anti-H3K4me3 | Millipore | Cat# 07–473; RRID: AB_1977252 |
| PE-conjugated anti-mouse CD40 Antibody | Biolegend | Cat# 124609; RRID: AB_1134084 |
| Anti-CDX2 antibody | Biogenex | Cat# NU777–5UC; RRID: N/A |
| Anti-MLL/HRX antibody, CT., clone 9–12 | Millipore | Cat# 05–765; RRID: AB_309977 |
| Anti-Oct-3/4 antibody (C-10) PE | Santa Cruz | Cat# sc-5279; RRID: AB_628051 |
| Anti-GC antibody | Thermo Fisher | Cat# PA5–29082; RRID: AB_2546558 |
| Anti-VDR (D-6) FITC-conjugated antibody | Santa Cruz | Cat# sc-13133 FITC |
| FITC-conjugated goat anti-rabbit IgG (H+L) cross adsorbed secondary antibody | Thermo Fisher | Cat# 31583; RRID: AB_228239 |
| Alexa Fluor® 555-conjugated goat anti-mouse IgG | Abcam | Cat# ab150114; RRID: AB_2687594 |
| Alexa Fluor Plus 647-conjugated goat anti-rabbit IgG highly cross-adsorbed secondary antibody, | Invitrogen | Cat# A32733; RRID: AB_2633282 |
| Alexa Fluor 488 Tyramide SuperBoost Kit, goat anti-mouse IgG | Thermo Fisher | Cat# B40941; RRID: N/A |
| 10-min. Tissue (Tumor) Dissociation / Single Cell Isolation Kit | 101Bio | Cat# P712–50; RRID: N/A |
|
Chemicals, Peptides, and Recombinant Proteins | ||
| ESGRO® leukemia inhibitory factor (LIF) | EMD Millipore | Cat# ESG1107 |
| Recombinant Human FGF-4 Protein | R&D Systems Inc. | Cat# 235-F4–025 |
| Heparin | Sigma-Aldrich | Cat# H3149 |
| KnockOut DMEM | Thermo Fisher | Cat# 10829018 |
| RPMI Media 1640 | Thermo Fisher | Cat# 11875–093 |
| Fetal bovine serum (FBS) | Atlas Biologicals | Cat# F-0500-D |
| KnockOut Serum Replacement | Thermo Fisher | Cat# 10828–028 |
| PD 0325901 | Sigma Aldrich | Cat# PZ0162 |
| CHIR99021 | Sigma Aldrich | Cat# SML1046 |
| 1α,25-Dihydroxyvitamin D3 | Sigma Aldrich | Cat# D1530 |
| Hygromycin | Sigma Aldrich | Cat# H3274 |
| Geltrex® Matrix Products | Thermo Fisher | Cat# A1413202 |
| KSOMaa EvolveR medium | Zenith Biotech | Cat# ZEKS-050 |
| Bovine Serum Albumin solution | SIGMA | Cat# A8412 |
| Mineral oil | SIGMA-ALDRICH | Cat# M8410 |
| EmbryoMax® 0.1% Gelatin Solution | Millipore | Cat# ES-006-B |
| VECTOR Red Alkaline Phosphatase (Red AP) Substrate Kit | Vector Laboratories | Cat# SK-5100 |
| FuGENE® 6 | Promega | Cat# E2691 |
| Normal Goat Serum | Cell Signaling Technology | Cat# 5425 |
|
Deposited Data | ||
| RNA-seq, ChIP–seq | This paper | GSE107408 |
| Single cell RNA-seq | This paper | GSE127943 |
| Flow cytometry | http://flowrepository.org/ | FR-FCM-Z29P |
|
Experimental Models: Organisms/Strains | ||
| Nagy ES cell line R1 with EGFP (D4) | MMRRC | Cat# 011980-MU |
| Mll1fl/fl;Cre-ERTM ESCs | Y. Dou | Zhang et al., 2016b |
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| H2B-Tomato E14Tg2a ESCs | J.M. Brickman | Morgani et al., 2013 |
| C57BL/6NCrl female mice | Charles River Laboratory | Cat# 493 |
| (C57BL/6J X SJL/J)F1 males | Jackson Laboratory | Cat# 100012 |
| Severe combined immunodeficiency (SCID) mice | Charles River Laboratory | Cat# 236-CB17SCID |
|
Oligonucleotides | ||
| GC siRNAs | Thermo Fisher | Cat# s66510 |
| GC siRNAs | Thermo Fisher | Cat# s66511 |
| Silencer® Negative Control No. 4 siRNA | Fisher | Cat# AM4641 |
| See STAR Methods for Primers for Real-time PCR | Integrated DNA Technologies | N/A |
|
Plasmids | ||
| 2C::tdTomato Reporter | Macfarlan et al., 2012 | Addgene #40281 |
| Flag-MLL1(full length) | Y. Dou | Dou et al., 2005 |
|
Software and Algorithms | ||
| Tophat2, v2.1.1 | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/manual.shtml |
| STEM, v1.3.11 | Wu et al., 2016 | http://www.cs.cmu.edu/~jernst/stem |
| Integrative Genomics Viewer (IGV), v2.3 | Thorvaldsdó ttir et al., 2013 | http://software.broadinstitute.org/software/igv/ |
| Cufflinks, v2.2.1 | Trapnell et al., 2012 | http://cole-trapnell-lab.github.io/cufflinks/ |
| CummeRbund, v2.1 | N/A | http://compbio.mit.edu/cummeRbund/ |
| Bowtie2, v2–2.2.4 | Langmead and Salzberg, 2012 | |
| MACS, v1.4.2 | Zhang et al., 2008 | http://liulab.dfci.harvard.edu/MACS/ |
| HOMER | Salk Institute | http://homer.salk.edu |
| GREAT, v3 | McLean et al., 2010 | http://great.stanford.edu/public/html/ |
| DeepTools2, v2.5.0 | Ramírez et al., 2016 | |
| Panther Classification System, v13.0 | N/A | http://pantherdb.org/ |
| GraphPad Prism, v7 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo, v10.0.7r2 | FlowJo LLC | http://docs.flowjo.com/d2/ |
| R, v3.4.3 | R foundation | https://cran.r-project.org/ |
| Cutadapt, V1.8.1 | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
| Fastq_screen, v0.5.1.4 | Babraham institute | http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ |
| STAR, v2.5.2b | Dobin et al., 2013 | https://code.google.com/archive/p/rna-star/ |
| Subread, v1.4.6-p1 | Liao et al., 2019 | http://subread.sourceforge.net/ |
| Seurat, V2.3.4 | Satija et al., 2015 | https://cran.r-project.org/web/packages/Seurat/index.html |
| Monocle, V2.6.1 | Trapnell et al., 2014 | http://cole-trapnell-lab.github.io/monocle-release/ |
| Ggplot2, V3.0.0 | Salk Institute | https://cran.r-project.org/web/packages/ggplot2/ |
|
Other | ||
| RNA-seq for pre-implantation embyos | Wu et al., 2016 | GEO: GSE66582 |
| RNA-seq for EpiSC reprograming | Zhang et al., 2016b | GEO: GSE66112 |