KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Anti-PAX6 | Biolegend | 901301, RRID: AB_256503 |
| Rabbit Anti-FOXG1 | Clontech | M227, RRID: AB_2827749 |
| Goat Anti-SP8 | Santa-Cruz | sc-104661, RRID: AB_2194626 |
| Mouse Anti-COUPTF-1 [H8132] | Abcam | ab41858 (discontinued) |
| Rabbit Anti-NKX2.1 | Abcam | ab76013, RRID: AB_10861200 |
| Rabbit Anti-SOX2 | Biolegend | 630802, RRID: AB_2195784 |
| Mouse Anti-PAX6 | BD Biosciences | 561462, RRID: AB_10715442 |
| Mouse Anti-ZO-1 | BD Biosciences | 610966, RRID: AB_398279 |
| Rabbit Anti-GSH2 | Millipore | ABN162, RRID: AB_11203296 |
| Mouse Anti-TBR2 | eBioscience | 14-4877-82, RRID: AB_2572882 |
| Mouse Anti-TUJ1 | Covance | MMS-435P, RRID: AB_2315514 |
| Mouse anti-Ki67 | DAKO | M724001 −2, RRID: AB_2631211 |
| Rabbit anti-NeuN | Cell Signaling Tech | 24307, RRID:AB_2651140 |
| Rat anti-CTIP2 | Abcam | Ab18465, RRID_2064130 |
| Rabbit anti-TBR1 | Abcam | Ab31940, RRID_AB2200219 |
| Mouse anti-SATB2 | Abcam | Ab51502, RRID_AB_882455 |
| Mouse anti-ISL1/2 | DSHB | 39.4D5, RRID_AB2314683 |
| Rabbit Anti-GABA | Sigma | A2052, RRID: AB_477652 |
| Mouse Anti-TBR2-FITC | eBioscience | 11-4877-42, RRID: AB_2572499 |
| Mouse Anti-DCX-PE | BD Biosciences | 561505, RRID: AB_10643766 |
| Mouse Anti-SOX2-A647 | BD Biosciences | 560302, RRID: AB_1645323 |
| Mouse Anti-CD49d-PE/Cy7 | Biolegend | 304314, RRID: AB_10643278 |
| Mouse anti-PAX6-A647 | BD Biosciences | 562249, RRID: AB_11152956 |
| Mouse anti-SSEA4-A647 | BD Biosciences | 560796, RRID: AB_2033991 |
| Mouse anti-OCT4-PE | BD Biosciences | 560186, RRID: AB_1645331 |
| AlexaFluor Donkey Anti-Goat 488 | Thermo Fisher Scientific | A-11055, RRID: AB_2534102 |
| AlexaFluor Donkey Anti-Goat 568 | Thermo Fisher Scientific | A-11057, RRID: AB_142581 |
| AlexaFluor Donkey Anti-Goat 647 | Thermo Fisher Scientific | A-21447, RRID: AB_141844 |
| 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-Rabbit 647 | Thermo Fisher Scientific | A-31573, RRID: AB_2536183 |
| 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 |
| AlexaFluor Donkey Anti-Mouse 647 | Thermo Fisher Scientific | A-21235, RRID: AB_141693 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DMEME:F12 w/ high glucose | Thermo Fisher Scientific | 11320–033 |
| 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 |
| Ascorbic Acid (AA) | Sigma Aldrich | 4034–100g |
| Recombinant human SHH (C24II) | R&D | 1845-SH |
| CHIR99021 (CHIR) | R&D | 4423 |
| Y-27632 (ROCKi) | R&D | 1254 |
| SB431542 (SB) | R&D | 1614 |
| LDN193189 (LDN) | Stem Cell Technologies | 72142 |
| XAV-939 (XAV) | R&D | 3746 |
| Recombinant human FGF8 | R&D | 423-F8 |
| Poly-L-Ornithine (PO) | Sigma Aldrich | P3655 |
| Mouse Laminin I (LAM) | R&D | 3400-010-1 |
| Fibronectin (FN) | Thermo Fisher Scientific | 356008 |
| Essential 8 (E8) | Thermo Fisher Scientific | A1517001 |
| Essential 6 (E6) | Thermo Fisher Scientific | A1516401 |
| 0.5M EDTA, pH 8.0 | Thermo Fisher Scientific | 15575020 |
| Accutase | Innovative Cell Technologies | AT104–500 |
| Vitronectin | Thermo Fisher Scientific | A14700 |
| Knockout Serum Replacement | Thermo Fisher Scientific | 10828–028 |
| Essential 8 FLEX | Thermo Fisher Scientific | A28558501 |
| Matrigel | BD Biosciences | 356234 |
| 50X B27 supplement w/o Vit A | Thermo Fisher Scientific | 17504044 |
| N2 supplement B | Stem Cell Technologies | 07156 |
| Recombinant human BMP4 | R&D | 314-BP |
| T rizol | Thermo Fisher Scientific | 15596026 |
| Dispase | Stemcell Technologies | 07913 |
| Progesterone | Sigma Aldrich | P8783 |
| Recombinant human FGF2 | R&D | 233-FB-001MG/CF |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | Qiagen | 74104 |
| SsoFast™ EvaGreen® Supermix | Bio-Rad | 172–5202 |
| iScript™ Reverse Transcription Supermix | Bio-Rad | 170–8841 |
| EdU Click-iT | Thermo Fisher Scientific | C10640 |
| Cytofix/Cytoperm Kit | BD Biosciences | 554722 |
| BD Perm/Wash Buffer | BD Biosciences | 554723 |
| ddPCR Supermix for probes no dUTP | Bio-Rad | 1863024 |
| Deposited Data | ||
| RNA-Seq | This study | NCBI GEO: GSE146760 |
| Experimental Models: Cell Lines | ||
| MEL-1 hESC line | Stem Cells Ltd | NIHhESC-11–0139 |
| Experimental Models: Organisms/Strains | ||
| Zebrafish | ab | ZDB-GENO-960809–7 |
| Oligonucleotides | ||
| See Supplemental Table 4 | N/A | N/A |
| Recombinant DNA | ||
| PX458 Cas9-GFP | Addgene | Addgene: 48138 |
| Software and Algorithms | ||
| Poly Peak Parser | http://yosttools.genetics.utah.edu/PolyPeakParser/ | N/A |
| ImageJ | https://imagej.nih.gov/ij/ | N/A |
| FlowJo 9 | http://www.flojo.com | N/A |
| DESeq2 | http://bioconductor.org/packages/release/bioc/html/DESeq2.html | (Love et al., 2014) |
| STAR 2.5.0 | https://github.com/alexdobin/STAR | N/A |
| R | https://cran.r-project.org/ | N/A |
| CHOPCHOP | http://chopchop.cbu.uib.no/ | N/A |
| Quantasoft (Bio-Rad) | https://www.bio-rad.com/en-us/sku/1864011-quantasoft-software-regulatory-edition?ID=1864011 | N/A |