Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Oct-4A (C30A3) Rabbit mAb | Cell Signaling Technologies | #2840 |
| Nanog (D73G4) XP® Rabbit mAb | Cell Signaling Technologies | #4903 |
| SSEA4 (MC813) Mouse mAb | Cell Signaling Technologies | #4755 |
| TRA-1-81 Mouse mAb | Cell Signaling Technologies | #4745 |
| Polyclonal Guinea Pig Anti-Insulin | Dako | #A0564 |
| Human SOX17 Antibody | R&D | AF1924 |
| Anti-HNF3β/FOXA2 Antibody | Millipore | 07-633 |
| Purified Rabbit Anti- Active Caspase-3 | BD bioscience | #559565 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | A-11055 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 | Thermo Fisher Scientific | A-214477 |
| Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H+L) | Jackson ImmunoResearch Labs | #706-545-148 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488 | Thermo Fisher Scientific | #A32790 |
| Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | #A-21203 |
| Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 594 conjugate | Thermo Fisher Scientific | #A-21207 |
| Chemicals, peptides, and recombinant proteins | ||
| Normocin | Invivogen | #ant-nr-2 |
| Y-27632 | MedchemExpress | #HY-10583 |
| Activin A | R&D Systems | #338-AC-500/CF |
| Recombinant Human KGF (FGF-7) Protein | Peprotech | #100-19-500UG |
| CHIR99021 | Cayman Chemical | #13122 |
| SANT-1 | Sigma Aldrich | #S4572-25MG |
| Retinoic acid | Sigma Aldrich | #R2625-500MG |
| LDN 193189 hydrochloride | Axon Medchem | #Axon 1509 |
| TPPB | Tocris Bioscience | #5343 |
| T3 hormone | Sigma Aldrich | #T6397-100MG |
| Zinc sulfate heptahydrate | Sigma Aldrich | #Z0251-100G |
| Heparin sodium salt | Sigma Aldrich | #H3149-1MU |
| γ-Secretase Inhibitor XX | Millipore | #565789-1MG |
| ALK5 Inhibitor II | Cayman Chemical | #14794 |
| L-Ascorbic acid | Sigma Aldrich | #A4544-100G |
| R428 | MedchemExpress | #HY-15150 |
| N-acetyl-L-cysteine | Sigma Aldrich | #A9165-5G |
| Trolox | Millipore | #648471 |
| Matrigel | Corning | #354234 |
| TWEEN® 20 | Sigma-Aldrich | #P9416 |
| APC Annexin V | BD Biosciences | # 550475 |
| Paraformaldehyde, 4% in PBS | Thermo Fisher Scientific | #J61899.AK |
| Penicillin and Streptomycin | Thermo Fisher Scientific | #10378016 |
| Fetal Bovine Serum, qualified, heat inactivated | Thermo Fisher Scientific | #10438026 |
| GlutaMAX | Thermo Fisher Scientific | #35050-061 |
| D-Glucose | Sigma-Aldrich | #G8769 |
| β-mercaptoethanol | Thermo Fisher Scientific | #21985023 |
| Nicotinamide | Sigma-Aldrich | #72340 |
| Sodium selenite | Sigma-Aldrich | #S9133 |
| Transferrin | Sigma-Aldrich | #T8158 |
| Accutase | Innovative Cell Technologies | #MSPP-AT104 |
| ReLeSR | STEMCELL Technologies | #05872 |
| ITS-X | Thermo Fisher Scientific | #51500056 |
| NaHCO3 | Thermo Fisher Scientific | #S6267 |
| Lipofectamine™ 2000 Transfection Reagent | Thermo Fisher Scientific | #11668027 |
| Opti-MEM | Thermo Fisher Scientific | #331985070 |
| Triton X-100 | Sigma-Aldrich | #X100 |
| Igepal CA-630 | Sigma-Aldrich | #I8896 |
| Digitonin | Promega | #G9441 |
| L-Ascorbic acid (vitamin C) | Sigma-Aldrich | #4544 |
| RIPA buffer | Sigma-Aldrich | #R0278 |
| BSA, Fatty Acid Free, Fraction V | Lampire | #7500804 |
| Bovine Serum Albumin, low endotoxin | Sigma-Aldrich | #A1470 |
| Lenti-X Concentrator | Takara | #631232 |
| Blasticidin | Thermo Fisher Scientific | #R21001 |
| Puromycin Dihydrochloride | Thermo Fisher Scientific | #A1113803 |
| EDTA | Thermo Fisher Scientific | #15575020 |
| DAPI | Sigma Aldrich | #D9542 |
| Critical commercial assays | ||
| Dual-Luciferase® Reporter Assay System | Promega | #E1980 |
| Nano-Glo® Luciferase Assay System | Promega | #N1130 |
| STELLUX Chemi Human Insulin ELISA Jumbo | Alpco | #80-INSHU-CH10 |
| High-Capacity cDNA Reverse Transcription Kit with RNase Inhibitor | Thermo Fisher Scientific | #4374966 |
| SYBR™ Green PCR Master Mix | Roche | #4309155 |
| Absolutely RNA Microprep Kit | Agilent Technologies | #400805 |
| RNeasy Plus Mini Kit | Qiagen | #74136 |
| Zymo DNA Clean & Concentrator Kits | Zymo Research | #D4003 |
| TruSeq Stranded mRNA LP (48 Spl) | Illumina | #20020594 |
| IDT for Illumina – TruSeq RNA UD Indexes (96 Indexes, 96 Samples) | Illumina | #20022371 |
| Illumina Tagment DNA Enzyme and Buffer Large Kit | Illumina | #20034198 |
| Deposited data | ||
| RNA-seq data | This paper | GSE228665 |
| ATAC-seq data | This paper | GSE228665 |
| SNP array genotyping data | This paper | GSE228665 |
| Whole genome sequence data | This paper | GSE228665 |
| Source data for manuscript figures | This paper | Table S1 |
| Experimental models: Cell lines | ||
| hESC line MEL-1 | Monash University | #CVCL_XA16 |
| EndoC-βH1 | INSERM | #CVCL_L909 |
| HEK293T cells | ATCC | #CRL-11268 |
| Oligonucleotides | ||
| Primers used for DNA sequencing | Integrated DNA Technologies | Sequences in Table S1 |
| Primers used for qRT-PCR | Integrated DNA Technologies | Sequences in Table S1 and Table S6 |
| Primers used for constructing luciferase vectors | Integrated DNA Technologies | Sequences in Table S6 |
| Recombinant DNA | ||
| pSpCas9(BB)-2A-Puro (PX459) V2.0 | Ran et al. 201319 | Addgene plasmid # 62988; RRID: Addgene_62988 |
| pCC_12 - hU6-BsmBI-sgRNA(E+F)-barcode-EFS-KRAB-dxCas9NG-NLS-2A-Puro-WPRE | Legut et al. 202082 | Addgene plasmid # 139097; RRID: Addgene_139097 |
| pCC_05 - hU6-BsmBI-sgRNA(E+F)-barcode-EFS-dCas9-NLS-VPR-2A-Puro-WPRE | Legut et al. 202082 | Addgene plasmid # 139090; RRID: Addgene_139090 |
| psPAX2 | Didier Trono83 | Addgene plasmid # 12260; RRID: Addgene_12260 |
| pMD2.G | Didier Trono84 | Addgene plasmid # 12259; RRID: Addgene_12259 |
| Proinsulin-NanoLuc in pLX304 | Burns et al. 201548 | Addgene plasmid # 62057; RRID: Addgene_62057 |
| pGL4.23[luc2/minP] vector | Promega | #E8411 |
| phRL-SV40 Vector | Promega | #E6261 |
| Software and algorithms | ||
| FlowJo | FLOWJO LLC | https://www.flowjo.com/ |
| GraphPad Prism | GraphPad Software | http://www.graphpad.com/scientific-software/prism |
| Adobe illustrator | Adobe | https://www.adobe.com/products/illustrator.html |
| MetaMorph® image analysis software | Molecular Devices | https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metamorph-microscopy |
| ZEN | ZEISS | https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html |
| novoalign v2.07.11 | http://www.novocraft.com/products/novoalign | |
| Michigan TOPmed Server (Minimac v4) | Das et al. 201685 | https://imputation.biodatacatalyst.nhlbi.nih.gov/#! |
| STAR v2.73a | Dobin et al. 201386 | https://github.com/alexdobin/STAR |
| QoRTs (v1.3.6,87 | Hartley & Mullikin 201587 | https://hartleys.github.io/QoRTs/ |
| GATK v4.1.9.0 | Auwera & O’Connor 202088 | https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices |
| Samtools v1.9 | Danecek et al. 202189,90 | https://github.com/samtools/samtools |
| verifybamID v1.1.191 | Jun et al. 201291 | https://github.com/statgen/verifyBamID/releases |
| BWA-MEM v0.7.17-r1194 | Li & Durbin 200992 | https://github.com/lh3/bwa |
| bedtools v2.26.0 | Quinlan and Hall 201093 | https://bedtools.readthedocs.io/en/latest/content/installation.html |
| MACS2 v2.2.7.194 | Zhang et al. 200894 | https://github.com/macs3-project/MACS/wiki/Install-macs2 |
| DESeq2 v1.32.095 | Love et al. 201495 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| MetaVolcano v1.10.096 | Cesar Prada 201996 | https://www.bioconductor.org/packages/release/bioc/html/MetaVolcanoR.html |
| fgsea v1.20.0 | Korotkevich et al. 201697 | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| msigdbr v7.5.1 | Liberzon et al. 201198 | https://igordot.github.io/msigdbreak/ |
| UCSC Genome Browser | Nassar et al. 202399 | https://genome.ucsc.edu/ |
| LIMIX v1.0.17 | Lippert et al. 2014100 | https://github.com/limix/limix/blob/master/doc/qtl.rst |
| CELLEX v1.2.2 | Timshel et al. 2020101 | https://github.com/perslab/CELLEX/blob/master/tutorials/demo_mousebrain_vascular_cells.ipynb |
| CTA: C++ implementation of Buenrostro adapter trimming | John Hensley 2017John Hensley 2017 | https://github.com/ParkerLab/cta |
| FIMO v5.4.1 | Grant et al. 2011102 | https://meme-suite.org/meme/doc/download.html |
| SEA v5.4.1 | McLeay & Bailey 2010103 | https://meme-suite.org/meme/doc/download.html |
| CENTIPEDE v1.2 | Pique-Regi et al. 2011104 | https://rdrr.io/rforge/CENTIPEDE/man/CENTIPEDE-package.html |
| WASP v0.3.4 | van de Geijn et al. 2015105 | https://github.com/bmvdgeijn/WASP |
| Annotate_variation.pl (v2019-10-24) | Wang et al. 2010106 | https://annovar.openbioinformatics.o |
| Other | ||