KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-OCT4 | Cell Signaling | CAT#C30A3; RRID AB_2167691 |
| Rat monoclonal anti-SOX2 | Thermo Fisher | CAT#14-9811-82; RRID AB_11219471 |
| Goat polyclonal anti-SOX17 | R&D Systems | CAT#AF1924; RRID AB_355060 |
| Rabbit monoclonal anti-pSMAD1/5/9 | Cell Signaling | CAT#12428; RRID: AB_2797908 |
| Rabbit monoclonal anti-pSMAD2 | Cell Signaling | CAT#18338; RRID: AB_2798798 |
| Mouse monoclonal anti-PAX6 | Developmental Studies Hybridoma Bank | CAT#PAX6; RRID: AB_528427 |
| Goat polyclonal anti-NANOG | R&D Systems | CAT#AF1997; RRID: AB_355097 |
| Rabbit monoclonal anti-CDH2 (NCAD) | Cell Signaling | CAT#13116; RRID: AB_2687616 |
| Bacterial and virus strains | ||
| NEB Stable competent E. coli | New England Biolabs | CAT#C3040 |
| Chemicals, peptides, and recombinant proteins | ||
| A 83-01 | R&D Systems | CAT#2939 |
| Human BMP4 | R&D Systems | CAT#314-BP |
| Human/Mouse/Rat Activin A Protein | R&D Systems | CAT#338-AC |
| γ-27632 | Stemgent | CAT#04-0012 |
| LDN-193189 | R&D Systems | CAT#6053 |
| Critical commercial assays | ||
| RNeasy Mini Kit | QIAGEN | CAT#74004 |
| KAPA mRNA Hyper Prep kit | Roche | CAT#07962363001 |
| Gibson Assembly Master Mix | New England Biolabs | CAT#E2611 |
| NEB Q5 High-Fidelity DNA Polymerase | NEB | CAT#M0491 |
| Deposited data | ||
| ATAC-seq | NCBI GEO | GSE149077 |
| RNA-seq | NCBI GEO | GSE148904 |
| Experimental models: cell lines | ||
| Human: H1 embryonic stem cells | WiCell | WA01, RRID CVCL_9771 |
| Human: H1 SOX2:YFP/OCT4:RFP embryonic stem cells | Zhang et al., 2019 | N/A |
| Oligonucleotides | ||
| Gibson homology arm to clone genes of interest into pWPXL-mCerulean-P2A, forward: gcaggtgacgtggaggagaatcccgggcct | This paper | N/A |
| Gibson homology arm to clone genes of interest into pWPXL-mCerulean-P2A, reverse: aatccagaggttgattatcatatga | This paper | N/A |
| Recombinant DNA | ||
| pWPXL | Addgene | CAT#12257; RRID: Addgene_12257 |
| pWPXL-mCerulean-P2A | This paper | N/A |
| pMD2.G | Addgene | CAT#12259; RRID: Addgene_12259 |
| psPAX2 | Addgene | CAT#12260; RRID: Addgene_12260 |
| Software and algorithms | ||
| Fiji | Schindelin et al., 2012 | https://imagej.net/software/fiji/ |
| MATLAB 2019 | MathWorks | https://www.mathworks.com/products/matlab.html |
| MicroManager 2.0 beta | Edelstein et al., 2014 | https://micro-manager.org |
| CellProfiler 3.0 | McQuin et al., 2018 | https://cellprofiler.org/ |
| DESeq2 1.24.0 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| kallisto 0.45.1 | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| chromVAR 1.4.1 | Schep et al., 2017 | https://github.com/GreenleafLab/chromVAR |
| MEME-ChIP 5.0.3 | Machanick and Bailey, 2011 | https://meme-suite.org/meme/tools/meme-chip |
| PANTHER | Mi et al., 2019 | http://www.pantherdb.org |
| Enrichr | Kuleshov et al., 2016 | https://maayanlab.cloud/Enrichr/ |
| GREAT | McLean et al., 2010 | http://great.stanford.edu/public/html/ |
| Other | ||
| hESC-qualified Matrigel | Corning | CAT#354277 |
| Polyester membrane filters, 3 micron, 25mm | Sterlitech | CAT#PET3025100 |
| mTeSR 1 | STEMCELL | CAT#85850 |
| Accutase | Innovative Stem Cell Technologies | CAT#AT104-500 |
| jetPrime | Polyplus | CAT#114-07 |
| Lenti-X Concentrator | Clontech | CAT#631231 |
| ENCODE RNA-seq data | ENCODE | See method details |