KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-4EBP1, phospho (Thr37/Thr46) | Cell Signaling | 2855; RRID:AB_560835 |
| Rabbit anti-AKT | Cell Signaling | 9272; RRID:AB_329827 |
| Rabbit anti-Phospho-AKT (Ser473) | Cell Signaling | 9271; RRID:AB_329825 |
| Goat anti-BRACHUYRY (T) | R&D | AF2085; RRID:AB_2200235 |
| Rabbit anti-p44/42 MAPK (ERK1/2) | Cell Signaling | 9102; RRID:AB_330744 |
| Rabbit anti-p44/42 MAPK (Phospho-ERK1/2) | Cell Signaling | 9101; RRID:AB_331646 |
| Rabbit anti-ESRRB | Millipore | ABD101 |
| Mouse anti-H3 | Abcam | ab24834; RRID:AB_470335 |
| Rabbit anti-H3K4me3 | Abcam | ab8580; RRID:AB_306649 |
| Rabbit anti-H3K9Ac | Abcam | ab4441; RRID:AB_2118292 |
| Rabbit anti-H3K9me3 | Abcam | ab8898; RRID:AB_306848 |
| Rabbit anti-H3K27Ac | Abcam | ab4729; RRID:AB_2118291 |
| Rabbit anti-H3K27me3 | Millipore | 07-449; RRID:AB_310624 |
| Rabbit anti-H4 | Abcam | ab70701; RRID:AB_1209472 |
| Rabbit anti-H4K8Ac | Abcam | ab15823; RRID:AB_880455 |
| Rabbit anti-LAMIN B1 | Abcam | ab16048; RRID:AB_443298 |
| Mouse anti-KLF4 | Santa Cruz | Sc-166238; RRID:AB_2130234 |
| Rabbit anti-KLF17 | Atlas Antibodies | HPA024629; RRID:AB_1668927 |
| Rabbit anti-mTOR (7C10) | Cell Signaling | 2983; RRID:AB_2105622 |
| Rabbit anti-Phospho-mTOR (Ser2448 D9C2) | Cell Signaling | 5536; RRID:AB_10691552 |
| Rabbit anti-NANOG (D73G4) | Cell Signaling | 4903; RRID:AB_10559205 |
| Mouse anti-OCT3/4 (C-10) | Santa Cruz | SC-5279; RRID:AB_628051 |
| Rabbit anti-PAX6 | Biolegend | PRB-278P; RRID:AB_291612 |
| Rabbit anti-Phospho-S6K p70 (Thr389) (108D2) | Cell Signaling | 9234; RRID:AB_2269803 |
| Rabbit anti-Phospho-S6K p70 (Ser371) | Cell Signaling | 9208; RRID:AB_330990 |
| Rat anti-SSEA3 | BD | 560237; RRID:AB_1645542 |
| Mouse anti-SSEA4 (MC813-70) | BD | 560796; RRID:AB_2033991 |
| Goat anti-SOX1 | R&D | AF3369; RRID:AB_2239879 |
| Mouse anti-SOX17 | R&D | MAB1924; RRID:AB_2195646 |
| Mouse anti-STELLA | Millipore | MAB4388; RRID:AB_2094156 |
| Goat anti-TFCP2L1 | R&D | AF5726; RRID:AB_2202564 |
| Rabbit anti-TFE3 | Sigma | HPA023881; RRID:AB_1857931 |
| Mouse anti-γ TUBULIN | Sigma | T6557; RRID:AB_477584 |
| AlexaFluor Donkey Anti-Goat 568 | Thermo Fisher Scientific | A-11057; RRID:AB_142581 |
| AlexaFluor Donkey Anti-Rabbit 488 | Thermo Fisher Scientific | A-21206; RRID:AB_141708 |
| AlexaFluor Donkey Anti-Rabbit 555 | Thermo Fisher Scientific | A-31572; RRID:AB_162543 |
| AlexaFluor Donkey Anti-Mouse 488 | Thermo Fisher Scientific | R37114; RRID:AB_2556542 |
| AlexaFluor Donkey Anti-Mouse 555 | Thermo Fisher Scientific | A-31570; RRID:AB_2536180 |
| Biological Samples | ||
| Mouse embryonic fibroblasts (MEF) | Thermo Fisher Scientific | A34959 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Knockout Serum Replacement (KSR) | Thermo Fisher Scientific | 10828-028 |
| DMEM-F12 | Thermo Fisher Scientific | 11320-032 |
| Essential 8 (E8) | Thermo Fisher Scientific | A1517001 |
| Essential 6 (E6) | Thermo Fisher Scientific | A1516401 |
| Knockout DMEM | Thermo Fisher Scientific | 10829-018 |
| mTeSR | StemCell Technologies, Inc. | 85850 |
| DMEM no glucose, no phenol red, no glutamine | Thermo Fisher Scientific | A14430 |
| AlbuMAX I Lipid-Rich BSA | Thermo Fisher Scientific | 11020021 |
| BSA fatty-acid free | Sigma Aldrich | A3803 |
| Chemically defined lipid concentrate | Thermo Fisher Scientific | 11905031 |
| L-Glutamine (100X) | Thermo Fisher Scientific | 25030-081 |
| Non-essential Amino Acids (100X) | Thermo Fisher Scientific | 11140-050 |
| Penicillin Streptomycin | Thermo Fisher Scientific | 15140-122 |
| 2-mercaptoethanol | Thermo Fisher Scientific | 21985-023 |
| Sodium Bicarbonate | Sigma Aldrich | S5761 |
| D-(+)-Glucose | Sigma Aldrich | G7021 |
| 2-Deoxy-D-glucose | Sigma Aldrich | D6134 |
| N2 supplement B | Stem Cell Technologies | 07156 |
| Progesterone | Sigma Aldrich | P8783 |
| Recombinant human FGF2 | R&D | 233-FB-001MG/CF |
| Recombinant human TGF-beta 1 | R&D | 240-B-002 |
| 0.5M EDTA, pH 8.0 | Thermo Fisher Scientific | 15575-020 |
| Dispase | Stem Cell Technologies | 07913 |
| Accutase | Innovative Cell Technologies | AT104-500 |
| Vitronectin (VTN-N) | Thermo Fisher Scientific | A14700 |
| Matrigel | Corning | 354234 |
| Normal Donkey Serum | Sigma Aldrich | S30 |
| Trypsin from Bovine Pancreas | Sigma Aldrich | T9935 |
| Soybean Trypsin inhibitor | Thermo Fisher Scientific | 17075029 |
| Y-27632 (ROCKi) | R&D | 1254 |
| SB431542 (SB) | R&D | 1614 |
| LDN193189 (LDN) | Stemgent | 04-0074 |
| PD0325901 | Stemgent | 04-0006 |
| BCI hydrochloride | Sigma Aldrich | B4313 |
| Fatostatin A | Tocris | 4444 |
| Critical Commercial Assays | ||
| Direct-zol RNA preparation kit | Zymo | R2062 |
| SsoFast Eva Green Supermix | Bio-Rad | 172-5200 |
| iScript Reverse Transcription Supermix | Bio-Rad | 170-8891 |
| nCounter custom codeset | Nanostring | N/A |
| Quick-DNA miniprep plus kit | Zymo Research | D4069 |
| DNeasy Blood and tissue kit | QIAGEN | 69504 |
| miRNeasy Mini Kit | QIAGEN | 217004 |
| miFinder miRNA PCR Array | QIAGEN | MIHS-122Z |
| ChIP DNA Clean and Concentrator | Zymo Research | D5205 |
| TMRE - Mitochondrial Membrane Potential Assay Kit | Abcam | ab113852 |
| CytoTune-iPS 2.0 Sendai Reprogramming Kit | Thermo Fisher Scientific | A16517 |
| Human Pluripotent Stem Cell Transcription Factor Analysis Kit | BD | 560589 |
| Human Mitochondrial DNA (mtDNA) Monitoring Primer Set | Takara | 7246 |
| Methylflash methylated DNA 5mC quantification kit | Epigentek | P1034 |
| RSet naive | Stem Cell Technologies | 05970 |
| NaiveCult | Stem Cell Technologies | 05580, 05590 |
| PSC Definitive Endoderm Induction Kit | Thermo Fisher Scientific | A3062601 |
| STEMdiff Mesoderm Induction Medium | Stem Cell Technologies | 05220 |
| Lipid (Oil Red O) staining kit | Biovision | K580-24 |
| NextFlex Bisulfite-Seq | Perkin Elmer | 5119-01 |
| truChIP Chromatin Shearing Kit | Covaris | 520154 |
| TruSeq Stranded Total RNA | Illumina | RS-122-2301 |
| Deposited Data | ||
| RNA Seq, ChIP Seq, WGBS | NCBI SRA | SRA: SRP104789 |
| Experimental Models: Cell Lines | ||
| H9 (WA-09) hESC line | WiCell Research Institute | NIHhESC-10-0062 |
| MEL1 hESC line | Stem Cells Ltd. | NIHhESC-11-0139 |
| HUES 6 hESC line | HSCI iPS Core | NIHhESC-09-0019 |
| 706 iPSC line | MSKCC Stem Cell Core | (Miller et al., 2013) |
| 036 iPSC line (parental line: primary fibroblasts) | iPSC: This study; pFIB: Coriell Institute | GM02036 |
| 731 iPSC line (parental line: primary fibroblasts) | iPSC: This study; pFIB: Coriell Institute | GM00731 |
| SeV6 iPSC line | MSKCC Stem Cell Core | (Kriksetal., 2011) |
| TLR3 iPSC line | Studer lab | (Lafaille et al., 2012) |
| Oligonucleotides – ChIP qPCR control primers | ||
| H3K27Ac+, H3K27me3− | N/A | |
| hsGAPDH E1 F: TCGACAGTCAGCCGCATCT; hsGAPDH I1 R: CTAGCCTCCCGGGTTTCTCT |
This study | N/A |
| hsRPL30 E1 F: CAAGGCAAAGCGAAATTGGT; hsRPL30 E1 R: GCCCGTTCAGTCTCTTCGATT |
This study | N/A |
| hsALDOA I2 F: TCCTGGCAAGATAAGGAGTTGAC; hsALDOA I2 R: ACACACGATAGCCCTAGCAGTTC |
This study | N/A |
| H3K27Ac−, H3K27me3+ | N/A | |
| hsMYOD E1 F: CCGCCTGAGCAAAGTAAATGA; hsMYOD E1 R: GGCAACCGCTGGTTTGG |
This study | N/A |
| hsSERPINA1 E1 F: GGCTCAAGCTGGCATTCCT; hsSERPINAI E1 R: GGCTTAATCACGCACTGAGCTTA |
This study | N/A |
| hsAFM I1 F: GCAGAACCTAGTTCCTCCTTCAAC; hsAFM I1 R: AGTCATCCCTTCCTACAGACTGAGA |
This study | N/A |
| Software and Algorithms | ||
| FIJI – ImageJ | (Schindelin et al., 2012) | https://fiji.sc/ |
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR/ |
| featureCounts | (Liao et al., 2014) | http://bioinf.wehi.edu.au/featureCounts/ |
| DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| DAVID | (Huang et al., 2009) | https://david.ncifcrf.gov/ |
| REVIGO | http://revigo.irb.hr/ | N/A |
| FLEXBAR | (Dodtetal., 2012) | https://github.com/seqan/flexbar |
| Bismark | (Krueger and Andrews, 2011) | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2 |
| MACS | (Zhang et al., 2008) | http://liulab.dfci.harvard.edu/MACS/ |
| DiffBind | http://bioconductor.org/packages/release/bioc/html/DiffBind.html | N/A |
| Other | ||
| Complete mini EDTAfree protease inhibitor | Roche | 11836170001 |
| Protein G Dynabeads | Thermo Fisher Scientific | 10003D |
| RNase A | Thermo Fisher Scientific | EN0531 |
| Proteinase K | Thermo Fisher Scientific | 25530-031 |
| DNA LoBind tubes | Eppendorf | 0030108051 |