KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-Glutamine Synthetase; 1/500 | BD Biosciences | Cat#610517; RRID:AB_2313837 |
| Rabbit anti-PAX6; 1/500 | Cell Signaling Technology | Cat#60433; RRID:AB_2797599 |
| Rabbit anti-Pyruvate Dehydrogenase E1-alpha subunit (phospho S293); 1/500 | Abcam | Cat#ab177461; RRID:AB_2756339 |
| Rabbit anti-Phospho-p70 S6 Kinase (Thr389) (108D2); 1/500 | Cell Signaling Technology | Cat#9234; RRID:AB_2269803 |
| Rabbit anti-p70 S6 Kinase (49D7); 1/500 | Cell Signaling Technology | Cat#2708; RRID:AB_390722 |
| Rabbit anti-OCT-4; 1/200 | Cell Signaling Technology | Cat#2750; RRID:AB_823583 |
| Mouse anti-OCT-4 (D7O5Z); 1/200 | Cell Signaling Technology | Cat#75463; RRID:AB_2799870 |
| Goat anti-human NANOG; 5 μg/mL | R&D Systems | Cat#AF1997; RRID:AB_355097 |
| Mouse anti-SOX2; 1/400 | Cell Signaling Technology | Cat#4900; RRID:AB_10560516 |
| Mouse anti-MAP2; 1/500 | Invitrogen | Cat#MA5-12826; RRID:AB_10976831 |
| Rabbit anti-OTX2; 4 μg/mL | Abcam | Cat#ab114138 |
| Goat anti-Brachyury/TBXT; 15 μg/mL | R&D Systems | Cat# AF2085; RRID:AB_2200235 |
| Rabbit anti-SLUG/SNAI2; 1/400 | Cell Signaling Technology | Cat#9585; RRID:AB_2239535 |
| Mouse anti-SOX17; 1/100 | Invitrogen | Cat#MA5-24891; RRID:AB_2725395 |
| Rabbit anti-FoxA2/HNF3β (D56D6); 1/400 | Cell Signaling Technology | Cat#8186; RRID:AB_10891055 |
| Mouse anti-β-tubulin; 1/1000 | Millipore Sigma | Cat#T4026; RRID:AB_477577 |
| Alexa Fluor 647 Rat Anti-Histone H3 (pS28) | BD Biosciences | Cat#558217; RRID:AB_397065 |
| APC anti-DYKDDDDK Tag Antibody | Biolegend | Cat#637308; RRID:AB_2561497 |
| PE Mouse Anti-SNAI2/Slug | BD Biosciences | Cat#564615; RRID:AB_2738866 |
| Alexa Fluor 488 Mouse Anti-Human Sox17 | BD Biosciences | Cat#562205; RRID:AB_10893402 |
| PerCPCy5.5 Mouse anti-Human PAX6 | BD Biosciences | Cat#562388; RRID:AB_11153319 |
| Alexa Fluor 488 Mouse anti-MAP2B | BD Biosciences | Cat#560399; RRID:AB_1645358 |
| PE Mouse anti-Human Sox1 | BD Biosciences | Cat#561592; RRID:AB_10714631 |
| Alexa Fluor 488 Mouse anti-Oct3/4 | BD Biosciences | Cat#560253; RRID:AB_1645304 |
| V450 Mouse Anti-Sox2 | BD Biosciences | Cat#561610; RRID:AB_10712763 |
| PerCP-Cy5.5 Mouse IgG2a, κ Isotype Control | BD Biosciences | Cat#558020; RRID:AB_396989 |
| Alexa Fluor 700 Mouse IgG1, κ Isotype Control | BD Biosciences | Cat#557882; RRID:AB_396920 |
| Alexa Fluor 488 Mouse IgG1 κ Isotype Control | BD Biosciences | Cat#557782; RRID:AB_396870 |
| PE Mouse IgG1 k Isotype Control | BD Biosciences | Cat#554680 RRID:AB_395506 |
| V450 Mouse IgG1, κ Isotype Control | BD Biosciences | Cat#560373; RRID:AB_1645606 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Fixable Viability Dye APC-Cy7 eFluor780 | Thermofisher | Cat#65-0865-14 |
| 7-AAD Staining Solution | BD Pharmingen | Cat#559925 |
| ActinRed™ 555 ReadyProbes® Reagent Protocol (Rhodamine phalloidin) | Invitrogen | Cat#R37112 |
| Gentle Cell Dissociation Reagent | Stemcell Technologies | Cat#07174 |
| mTeSR1 Plus | Stemcell Technologies | Cat#05825 |
| DMEM/F12 | Gibco | Cat#11320033 |
| ROCK Inhibitor; Y-27632 | Stemcell Technologies | Cat#72304 |
| Monothioglycerol | Millipore Sigma | Cat#M6145 |
| BSA Fraction V, 7.5% | Gibco | Cat#15260037 |
| 2-mercaptoethanol | Thermofisher | Cat#21985-023 |
| GlutaMAX Supplement | Thermofisher | Cat#35050-061 |
| N2 Supplement | Gibco | Cat#17502048 |
| B27 Supplement | Gibco | Cat#17504044 |
| SB43154 | Stemgent | Cat#04-0010 |
| Dorsomorphin | Stemgent | Cat#04-0024 |
| Human Recombinant Insulin | Millipore Sigma | Cat#11376497001 |
| Transferrin from human serum | Millipore Sigma | Cat#10652202001 |
| Chemically Defined Lipid Concentrate (CDLC) | Gibco | Cat#11905031 |
| Human Recombinant VEGF-165 | Stemcell Technologies | Cat#78073.1 |
| Human Recombinant BMP-4 | PeproTech | Cat#120-05ET |
| Human Recombinant FGF2 | Stemcell Technologies | Cat#78003 |
| Human Recombinant Activin A | Stemcell Technologies | Cat#78001.1 |
| CHIR99021 (GSK3i) | Stemcell Technologies | Cat#72052 |
| PI-103 Hydrochloride | Tocris/Fisher Scientific | Cat#29-301 |
| Stemolecule LDN-1931189 | Stemgent | Cat#04-0074 |
| 10% Fetal Bovine Serum | Omega Scientific | Cat#FB-11 |
| MEM Non-Essential Amino Acids | Gibco | Cat#11140-050 |
| Matrigel | Corning/Fisher Scientific | Cat#CB-4023A |
| RNAse-Free DNase Set | Qiagen | Cat#79254 |
| DMEM/F12, no glutamine | Gibco | Cat#21331020 |
| L-GLUTAMINE (AMIDE-15N, 98%) | Cambridge Isotope Laboratories | Cat#NLM-577 |
| DPBS 1x w/o calcium & magnesium | Corning | Cat#21031CV |
| L-methionine sulfoximine | Millipore Sigma | Cat#91016 |
| Dimethyl 2-oxoglutarate | Millipore Sigma | Cat#ES-008 |
| Glucosamine 6-phosphate | Millipore Sigma | Cat#G5509 |
| L-Glutathione reduced | Millipore Sigma | Cat#G6529 |
| Ammonium Chloride | Millipore Sigma | Cat#A9434 |
| 6-Diazo-5-oxo-L-norleucine | Millipore Sigma | Cat#D2141 |
| CB-839 | Selleckchem | Cat#S7655 |
| 1x BD Perm/Wash Buffer | BD Biosciences | Cat#554714 |
| SYBR Green | Roche | Cat#04887352001 |
| 1x protease inhibitor | Sigma | Cat#P8340 |
| 1x phosphatase inhibitor | Sigma | Cat#P5726 |
| 1x phosphatase inhibitor | Sigma | Cat#P0044 |
| Odyssey Blocking Buffer TBS | Li-Cor | Cat#927-50010 |
| DMEM with L-Glutamine and Sodium Pyruvate | Corning | Cat#MT10013CV |
| OptiMEM | Gibco | Cat#11058021 |
| Fugene | Promega | Cat#E2312 |
| Non Essential Amino Acids | Gibco | Cat#1140 |
| Lenti-X Concentrator | Clontech | Cat#631231 |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | Qiagen | Cat#74106 |
| Fixation/Permeabilization Solution Kit | BD Biosciences | Cat#555028 |
| iSCRIPT cDNA Synthesis Kit | Bio-Rad | Cat#1708841 |
| MycoAlert Detection Kit | Lonza | Cat#LT08-418 |
| BCA Protein Assay Kit | Pierce/Thermofisher | Cat#23225 |
| Deposited Data | ||
| RNA-Sequencing Data for Nutrient Balanced hPSC and Trilineage Differentiation to EN/EC/ME | (Lu et al., 2019) | GEO: GSE127270 |
| UHPLC-MS quantification of intracellular abundance of metabolites. | This Manuscript | Supplemental Table S1 |
| Experimental Models: Cell Lines | ||
| H9 (WA09); Female | UCLA BSCRC hESC Core Bank | RRID:CVCL_9773 |
| UCLA-1; Female | UCLA BSCRC hESC Core Bank | RRID:CVCL_9951 |
| HEK293FT | Life Technologies | Cat#31985 |
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Primers for RT-qPCR, see Method Details | IDT | N/A |
| Recombinant DNA | ||
| pLKO-shGLUL-1 | Sigma-Aldrich | SHCLNG-NM 002065 TRCN0000343991 |
| pLKO-shGLUL-2 | Sigma-Aldrich | SHCLNG-NM 002065, TRCN0000343992 |
| shRNA NTC (non-mammalian turboGFP) | N/A | Addgene: SH202 |
| pCMV-VSV-G | Laboratory of Robert Weinberg(Stewart et al., 2003) | Addgene: 8454 |
| pCMV-dR8.2 dvpr | Laboratory of Robert Weinberg(Stewart et al., 2003) | Addgene: 8455 |
| pLJM1 FLAG Raptor Rheb 15 | Laboratory of David Sabatini(Sancak et al., 2010) | Addgene: 26634 |
| pLJM1 FLAG Raptor | Laboratory of David Sabatini(Sancak et al., 2010) | Addgene: 26633 |
| pLJM1 Empty | Laboratory of Joshua Mendell(Golden et al., 2017) | Addgene: 91980 |
| Software and Algorithms | ||
| Seahorse Wave Desktop Software | Agilent Technologies | https://www.agilent.com/en/products/cell-analysis/cell-analysis-software/data-analysis/wave-desktop-2-6 |
| Leica Application Suite (LAS) X Software | Leica Microsystems | https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Salmon v0.9.1 | (Patro et al., 2017) | https://combine-lab.github.io/salmon/ |
| Tximport v1.6.0 | (Soneson et al., 2015) | http://bioconductor.org/packages/release/bioc/html/tximport.html |
| DESeq2 v1.18.1 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| MitoMiner v4.0 | (Calvo et al., 2016) | http://mitominer.mrc-mbu.cam.ac.uk/release-4.0/begin.do |
| Pheatmap v1.0.8 | (Kolde, 2015) | https://github.com/raivokolde/pheatmap |
| Gplots v3.0.1 | (Gregory Warnes, 2016) | https://cran.r-project.org/web/packages/gplots/index.html |
| GSVA v1.26.0 | (Hanzelmann et al., 2013) | https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| Prism 7 and 8 | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| TraceFinder v3.3 | Thermofisher | https://www.thermofisher.com/order/catalog/product/OPTON-30491 |
| Limma v3.34.9 | (Ritchie et al., 2015) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| R v3.4.4 | The R Project for Statistical Computing | https://www.r-project.org |
| Bioconductor v3.6 | (Huber et al., 2015) | https://www.bioconductor.org |
| Other | ||