KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal Anti-CAS9 | Abcam | ab191468, RRID:AB_2692325 |
| Mouse monoclonal Anti-GAPDH | EMD Millipore Corp | CB1001–500UG, RRID:AB_2107426 |
| Mouse monoclonal Anti-MAP2 | Sigma-Aldrich | M-1406, RRID:AB_477171 |
| Mouse monoclonal Anti-SYNAPSIN-I | SantaCruz Biotech | sc-376623, RRID:AB_11150313 |
| Mouse monoclonal Anti-SOX2 | SantaCruz Biotech | sc-365823, RRID:AB_10842165 |
| Rat monoclonal Anti-CTIP2 | Abcam | ab18465 RRID:AB_2064130 |
| Mouse monoclonal Anti-OCT-4 | SantaCruz Biotech | sc-5279, RRID:AB_628051 |
| Rabbit polyclonal Anti-NANOG | Abcam | ab80892, RRID:AB_2150114 |
| Rabbit polyclonal Anti- PAX6 | Biolegend | 901301, RRID:AB_2565003 |
| Rabbit polyclonal Anti-TBR1 | Abcam | ab31940, RRID:AB_2200219 |
| Rabbit polyclonal Anti-TBR2 | EMD Millipore Corp | AB2283, RRID:AB_10806889 |
| Rabbit polyclonal Anti-SATB2 | Sigma-Aldrich | HPA001042, RRID:AB_10601711 |
| Mouse monoclonal Anti-Vimentin | Dako | M0725, RRID:AB_10013485 |
| Rabbit monoclonal Caspase 3 | Abcam | Ab32351, RRID:AB_725946 |
| Rabbit monoclonal KI67 | Invitrogen | MA5–14520, RRID:AB_10979488 |
| AlexaFluor Goat Anti-Mouse 488 | Thermo Fischer Scientific | R37120, RRID:AB_2556548 |
| AlexaFluor Goat Anti-Rabbit 488 | Thermo Fischer Scientific | A32731, RRID:AB_2633280 |
| AlexaFluor Goat Anti-Rat 488 | Abcam | ab150157, RRID:AB_2722511 |
| AlexaFluor Goat Anti-Mouse 594 | Abcam | ab150116, RRID:AB_2650601 |
| AlexaFluor Goat Anti-Rabbit 594 | Thermo Fischer Scientific | A11012, RRID:AB_141359 |
| AlexaFluor Goat Anti-Rat 568 | Thermo Fischer Scientific | A-11077, RRID:AB_141874 |
| AlexaFluor Goat Anti-Rabbit 647 | Thermo Fischer Scientific | A-27040, RRID:AB_2536101 |
| Bacterial and Virus Strains | ||
| E-coli XL10 Gold | Agilent Technologies | 200315 |
| E-coli subcloning efficiency DH5α | Thermofischer Scientific | 18265017 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DMEM | Thermo Fischer Scientific | 21063–029 |
| Fetal Bovine Serum (FBS) | Thermo Fischer Scientific | 10500–064 |
| 0.05%Trypsin-EDTA | Thermo Fischer Scientific | 25300–054 |
| Knockout Serum (KSR) | Thermo Fischer Scientific | 10828010 |
| DMEM-F12 (1:1) Ham | Thermo Fischer Scientific | 11320–033 |
| Essential 8 Flex basal media+ E8 Flex supplement (E8 flex) | Thermo Fischer Scientific | A2858501 |
| Essential 6 media (E6) | Thermo Fischer Scientific | A15165–01 |
| Neurobasal media (NB) | Thermo Fischer Scientific | 21103–049 |
| L-Glutamine (100X) | Thermo Fischer Scientific | 25030–024 |
| N2 supplement (100X) | Thermo Fischer Scientific | 17502–048 |
| N2 supplement B (100X) | StemCell Technologies | 07156 |
| B27 supplement – Vitamin A (50X) | Thermo Fischer Scientific | 12587–010 |
| MEM NEAA | Thermo Fischer Scientific | 11140050 |
| Penicillin/Streptomycin (100x) | Thermo Fischer Scientific | 15140–122 |
| Sodium Pyruvate (100x) | Thermo Fischer Scientific | 11360070 |
| 2-mercaptoethanol (1000X) | Thermo Fischer Scientific | 21985–023 |
| StemCell Pro Accutase | Thermo Fischer Scientific | A11105–01 |
| Sodium Bicarbonate | Sigma-Aldrich | S5761 |
| 0.5M EDTA (pH-8.0), Molecular biology grade | Promega | V4231 |
| Dimethyl Sulfoxide (DMSO) | PanReac Applied Chem | A3672–0250 |
| LDN193189 (LDN) | Stemgent | 04–0074 |
| SB431542 (SB) | Tocris | 1614 |
| XAV-939 (XAV) | Tocris | 3748 |
| Y-27632 dihydrochloride (ROCKi) | Tocris | 1254 |
| CHIR99021 (CHIR) | Tocris | 4423 |
| DAPT | Tocris | 2634 |
| Recombinant Sonic hedgehog (Shh) | R&D biosystems | 464-SH-200 |
| Recombinant Brain-derived Neurotrophic Factor (BDNF) | R&D biosystems | 248-BD-025 |
| Recombinant Glial-Derived Neurotrophic Factor (GDNF) | PeproTech | 450–10 |
| Ascorbic Acid (AA) | Sigma-Aldrich | A4034–100G |
| db c-AMP | Sigma-Aldrich | D0627–100MG |
| TGFβ3 | R&D Systems | 243-B3 |
| Human Insulin | Sigma-Aldrich | I-034 |
| D-(+)-glucose | Sigma-Aldrich | G7021 |
| Progesterone | Sigma-Aldrich | P8783–5G |
| Mouse Laminin I (LAM) | R&D biosystems | 3400-010-1 |
| Human Fibronectin (FN) | EMD Millipore Corp | FC010 |
| Poly-L-Ornithine hydrobromide (PO) | Sigma-Aldrich | P3655 |
| Recombinant Vitronectin (r-VTN) | Thermo Fischer Scientific | A14700 |
| Matrigel | Corning | 353234 |
| GelTrex | Thermo Fischer Scientific | A14133–02 |
| Absolute Ethanol (200 proof) molecular biology grade | Fischer Scientific | BP2818–500 |
| Puromycin dihydrochloride cell culture grade | Sigma-Aldrich | P8833 |
| Geneticin G418 | Thermo Fischer Scientific | 10131027 |
| Polybrene | Sigma-Aldrich | H9268 |
| DAPI | Thermo Fischer Scientific | D1306 |
| O.C.T compound | VWR chemicals | 361603E |
| Richard-Allan Scientific Blue NEG-50 | Thermo Fischer Scientific | 6502B |
| Immu-mount | Thermo Fischer Scientific | 9990412 |
| Trizol | Thermo Fischer Scientific | 15596026 |
| BfuA1 | New England Biolabs | R0701S |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | Qiagen | 74104 |
| QIAamp DNA mini kit | Qiagen | 51306 |
| Nucleospin Plasmid kit | Macherey-Nagel | 740588.50 |
| Nucleobond PC 500 Plasmid Maxi Kit | Macherey-Nagel | 740574.25 |
| Nucleospin Gel and PCR clean up | Macherey-Nagel | 740609.50 |
| Promega GoTaq Polymerase Kit | Promega | M300 |
| Superscript First strand cDNA synthesis Kit | Thermo Fischer Scientific | 11904–018 |
| Agilent RNA 6000 Nano Kit | Agilent Technologies | 5067–1511 |
| Deposited Data | ||
| RNA seq | This study | GEO: GSE171101 |
| Experimental Models: Cell Lines | ||
| H9 dCas9-VP64 | This study | |
| H9 dCas9-KRAB | This study | |
| H9 TRE-dCas9-VP64 | This study | |
| H9 HERV-K dCas9-VP64 | This study | |
| H9 control gRNA dCas9-VP64 | This study | |
| H9 HERV-K dCas9-KRAB | This study | |
| H9 control gRNA dCas9-KRAB | This study | |
| H9 HERV-K TRE-dCas9-VP64 | This study | |
| H9 control gRNA TRE-dCas9-VP64 | This study | |
| H9 CHRDL1 dCas9-VP64 | This study | |
| H9 CLSTN2 dCas9-VP64 | This study | |
| H9 EPHA4 dCas9-VP64 | This study | |
| H9 NTRK3 dCas9-VP64 | This study | |
| HEK 293T | ATCC | 293T/17(HEK293T/17) ATCC®CRL-11268™ |
| Oligonucleotides | ||
| gRNAs | This study | provided in Table S2 |
| qRT-PCR Primers | This study | provided in Table S3 |
| Recombinant DNA | ||
| pLKO.1- U6 sgRNA BfuA1 stuffer | Addgene plasmid #50920 | A gift from Rene Maehr & Scot Wolfe |
| pHAGE EFIα dCas9-VP64 | Addgene plasmid #50918 | A gift from Rene Maehr & Scot Wolfe |
| pHAGE EFIα dCas9-KRAB | Addgene plasmid #50919 | A gift from Rene Maehr & Scot Wolfe |
| pHAGE TRE-dCas9-VP64 | Addgene plasmid #50916 | A gift from Rene Maehr & Scot Wolfe |
| psPAX.2 | Addgene plasmid #12260 | A gift from Didier Trono |
| pMD2.G | Addgene plasmid #12259 | A gift from Didier Trono |
| NTRK3 MISSION® shRNA | TRCN0000194821 | Sigma-Aldrich |
| MISSION® pLKO.1-puro Non-Mammalian shRNA Control | SHC002 | Sigma-Aldrich |
| pLKO.1- U6 HERV-K(HML-2) G3 | This study | |
| pLKO.1- U6 HERV-K(HML-2) G10 | This study | |
| pLKO.1- U6 HERV-K(HML-2) G6 | This study | |
| pLKO.1- U6 HERV-K(HML-2) G11 | This study | |
| pLKO.1- U6 CHRDL1 G1 | This study | |
| pLKO.1- U6 CHRDL1 G7 | This study | |
| pLKO.1- U6 CLSTN2 G3 | This study | |
| pLKO.1- U6 CLSTN2 G23 | This study | |
| pLKO.1- U6 EPHA4 G2 | This study | |
| pLKO.1- U6 EPHA4 G11 | This study | |
| pLKO.1- U6 NTRK3 G1 | This study | |
| pLKO.1- U6 NTRK3 G17 | This study | |
| Software and Algorithms | ||
| Graph Pad prism 8 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Image J | NIH | https://imagej.nih.gov/ij/ |
| Adobe Photoshop (CC) | Adobe Inc. | https://www.adobe.com/products/photoshop.html |
| Adobe Illustrator (CC) | Adobe Inc. | https://www.adobe.com/products/illustrator.html |
| Snapgene Viewer | Insightful Science | www.snapgene.com |
| Optimised CRISPR design tool | Zhang Lab, MIT | www.crispr.mit.edu |
| CRISPR-ERA | Lei Stanley Qi Lab, Xiaowo Wang Lab, Stanford | http://crispr-era.stanford.edu |
| LC480 SW 1.5.1 | Roche | https://lifescience.roche.com/en_de/products/lightcycler14301-480-software-version-15.html |
| Zeiss AX10- Zen Pro 2.3 Blue | Zeiss | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html |
| STAR package | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| GENCODE database version 27 | (Harrow et al., 2012) | https://www.gencodegenes.org/human/release_29.html |
| featureCounts software | (Liao et al., 2014) | http://bioinf.wehi.edu.au/featureCounts/ |
| fastp software | (Chen et al., 2018) | https://github.com/OpenGene/fastp |