KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-PAX6 | Biolegend | Cat#901301; RRID: AB_256503 |
| Mouse monoclonal anti-Tyrosine Hydroxylase, clone LNC1 | Millipore | Cat#MAB318; RRID:AB_2201528 |
| Rabbit polyclonal anti-LMX-1 | Millipore | Cat#AB10533; RRID: AB_10805970 |
| Goat Anti-OTX2 | Neuromics | Cat#GT15095-100; RRID: AB_2157174 |
| Chicken polyclonal anti-MAP2 | Abcam | Cat# ab5392; RRID:AB_2138153 |
| Rabbit polyclonal anti-TH | PelFreez Biologicals | Cat#P40101-150; RRID:AB_2617184 |
| Mouse monoclonal anti-Ki-67 antigen (clone MIB-1) | Agilent | Cat# M724001-2, RRID:AB_2631211 |
| Goat polyclonal anti-FOXA2 | R&D Systems | Cat# AF2400; RRID:AB_2294104 |
| Mouse monoclonal anti-NURR1 | Perseus Proteomics | Cat# PP-N1404-00; RRID:AB_2251476 |
| Mouse monoclonal anti-EN1 | DSHB | Cat#4G11; RRID: AB_528219 |
| Rabbit polyclonal anti-Calbindin D-28k | Swant | Cat#CB38; RRID: AB_2721225 |
| Mouse monoclonal anti-STEM121 | Takara Bio Inc | Cat#AB-121-U-050; RRID: AB_2632385 |
| Goat anti-ALDH1A1 | Santa Cruz Biotechnology | Cat#sc-22588; RRID:AB_2289311 |
| Rabbit polyclonal anti-Synapsin I | Sigma-Aldrich | Cat#S193; RRID:AB_261457 |
| Rabbit polyclonal anti-Serotonin (5-HT) | Sigma-Aldrich | Cat#S5545; RRID: AB_477522 |
| Rabbit polyclonal anti-GIRK2 | Alomone labs | Cat#APC-006; RRID:AB_2040115 |
| Mouse monoclonal anti-human nuclei | Millipore | Cat#MAB1281; RRID: AB_94090 |
| Rabbit polycolnal anti-EN1 | Thermo Fisher Scientific | Cat#PA5–84917; RRID:AB_2792066 |
| Rabbit polyclonal anti-H3K27me3 | Millipore | Cat#07–449; RRID:AB_310624 |
| Rabbit polyclonal to Histone H3 (tri methyl K4) | Abcam | Cat#ab8580; RRID:AB_306649 |
| HRP-linked donkey anti–rabbit IgG | GE Healthcare | Cat# NA934; RRID:AB_772206 |
| HRP-linked anti-Goat IgG (H+L) | Invitrogen | Cat# A15999; RRID:AB_2534673 |
| HRP-linked sheep anti–mouse IgG | GE Healthcare | Cat: NA931; RRID:AB_772210 |
| AlexaFluor Donkey Anti-Goat 488 | Thermo Fisher Scientific | Cat#A-11055; RRID: AB_2534102 |
| AlexaFluor Donkey Anti-Goat 568 | Thermo Fisher Scientific | Cat#A-11057; RRID: AB_142581 |
| AlexaFluor Donkey Anti-Goat 647 | Thermo Fisher Scientific | Cat#A-21447; RRID: AB_141844 |
| AlexaFluor Donkey Anti-Rabbit 488 | Thermo Fisher Scientific | Cat#A-21206; RRID: AB_141708 |
| AlexaFluor Donkey Anti-Rabbit 555 | Thermo Fisher Scientific | Cat#A-31572; RRID: AB_162543 |
| AlexaFluor Donkey Anti-Rabbit 647 | Thermo Fisher Scientific | Cat#A-31573; RRID: AB_2536183 |
| AlexaFluor Donkey Anti-Mouse 488 | Thermo Fisher Scientific | Cat#R37114; RRID: AB_2556542 |
| AlexaFluor Donkey Anti-Mouse 555 | Thermo Fisher Scientific | Cat#A-31570; RRID: AB_2536180 |
| AlexaFluor Donkey Anti-Mouse 647 | Thermo Fisher Scientific | Cat#A-21235; RRID: AB_141693 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Vitronectin (VTN-N) | Thermo Fisher Scientific | A14700 |
| Trizol | Thermo Fisher Scientific | 15596026 |
| Recombinant human FGF8b | R&D | 423-F8 |
| Accutase | Innovative Cell Technologies | AT104–500 |
| 0.5M EDTA, pH 8.0 | Thermo Fisher Scientific | 15575–020 |
| L-Glutamine (100X) | Thermo Fisher Scientific | 25030–081 |
| Penicillin Streptomycin | Thermo Fisher Scientific | 15140–122 |
| Essential 8 (E8) | Thermo Fisher Scientific | A1517001 |
| Neurobasal | Life Technologies | 21103–049 |
| N2 supplement B | Stem Cell Technologies | 7156 |
| B27 | Life Technologies | 12587–010 |
| Y-27632 (ROCKi) | R&D | 1254 |
| SB431542 (SB) | R&D | 1614 |
| LDN193189 (LDN) | Stemgent | 04–0074 |
| CHIR99021 | R&D | 4432 |
| SHH C25II | R&D | 464-SH |
| brain-derived neurotrophic factor (BNDF) | R&D | 248-BD |
| ascorbic acid (AA) | Sigma | 4034 |
| dibutyryl cAMP (cAMP) | Sigma | 4043 |
| glial cell line-derived neurotrophic factor (GDNF) | Peptrotech | 450–10 |
| transforming growth factor type β3 (TGFβ3) | R&D | 243-B3 |
| DAPT | R&D | 2634 |
| Poly-L-Ornithine (PO) | Sigma Aldrich | P3655 |
| Mouse Laminin I (LAM) | R&D | 3400–010-1 |
| Fibronectin (FN) | Thermo Fisher Scientific | 356008 |
| Geltrex | Life Technologies | A1413201 |
| STEM-CELLBANKER™ | Amsbio | 11890 |
| 4% paraformaldehyde | Affymetrix | MFCD00133991 |
| 4′, 6-diamidino-2-phenylindole (DAPI) | Sigma | D9542 |
| Critical Commercial Assays | ||
| RNA MiniPrep kit | Zymo Research | R2052 |
| SsoFast EvaGreen® Supermix | Bio-Rad | 172–5202 |
| iScript Reverse Transcription Supermix | Bio-Rad | 170–8841 |
| SimpleChIP® Plus Enzymatic Chromatin IP Kit | Cell signaling Tech | 9005 |
| BD Perm/Wash Buffer | BD Biosciences | 554723 |
| BCA protein assay kit | Pierce | 23228 |
| Deposited Data | ||
| RNA-Seq | This study | GSE162884 |
| ChIP-Seq | This study | GSE162884 |
| Experimental Models: Cell Lines | ||
| Human: H9 (WA-09) hESC line | WiCell Research Institute | NIHhESC-10–0062 |
| MEL-1 hESC line | Stem Cells Ltd | NIHhESC-11–0139 |
| MRC5 (J1) iPSC line | MSKCC Stem Cell Core | Miller et al., 2013 |
| Oligonucleotides | ||
| See Table S1 | ||
| Recombinant DNA | ||
| PX458 Cas9-GFP | Addgene | Addgene: 48138 |
| Software and Algorithms | ||
| DESeq2 | Love et al., 2014 | http://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| R | https://cran.r-project.org/ | N/A |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2 |
| STAR aligner (v.2.4.2a) | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| FLEXBAR (v.2.2) | (Dodt et al., 2012) | https://github.com/seqan/flexbar |
| FeatureCounts (v.1.4.2) | (Liao et al., 2014) | http://bioinf.wehi.edu.au/featureCounts/ |
| MACS | (Zhang et al., 2008) | http://liulab.dfci.harvard.edu/MACS/ |
| CRISPR design tool | (http://crispr.mit.edu) | N/A |
| FIJI – ImageJ | (Schindelin et al., 2012) | https://fiji.sc/ |
| FlowJo 9 | http://www.flojo.com | N/A |
| Integrative Genomics Viewer (IGV) | Robinson et al., 2011 | http://software.broadinstitute.org/software/igv/ |
| Picardtools (version 2.9.5) | , Broad Institute | http://broadinstitute.github.io/picard/ |