Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti CTCF (clone D31H2) | Cell signaling technologies | 3418 |
| Rabbit anti H3K27ac | Active motif | 39133 |
| Rabbit anti PDGFRA | Cell signaling technologies | 3174 |
| Rabbit anti CDKN2A (p19 ARF) | Millipore | 07-543 |
| Mouse anti TP53 | Cell signaling technologies | 2524 |
| beta-actin-HRP conjugated | Sigma | A3854 |
| anti-rabbit IgG-HRP | Cell signaling technologies | 7074 |
| anti-mouse IgG-HRP | Cell signaling technologies | 7076 |
| Rabbit anti-Ki67 (D3B5) | Cell signaling technologies | 12202 |
| Rabbit anti Olig2 | Millipore | AB9610 |
| Rabbit anti CD31 | Cell signaling technologies | 77699 |
| Rabbit anti Glial Fibrillary acidic protein | Agilent Dako | Z0334 |
| Bacterial and virus strains | ||
| NEB stable competent E. coli | New England Biolabs | C3040I |
| Biological samples | ||
| Human IDH wild-type and IDH mutant glioma samples | Flavahan et al. 2016 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| ESGRO Leukemia Inhibitory Factor (LIF) | Millipore | ESG1107 |
| HyClone Fetal Bovine Serum (U.S.), Embryonic Stem (ES) Cell Screened | Hyclone | SH30070.02E |
| Recombinant Human EGF Protein | R&D Systems | 236-EG-200 |
| Recombinant Human FGF basic/FGF2 | R&D Systems | 4114-TC-01M |
| N-2 Supplement (100X) | GIBCO | 17502048 |
| B-27 Supplement (50X), serum free | GIBCO | 17504044 |
| GlutaMAX Supplement | GIBCO | 35050061 |
| Penicillin-Streptomycin | GIBCO | 15140122 |
| MEM Non-Essential Amino Acids Solution (100X) | GIBCO | 11140050 |
| L-Glutamine (200 mM) | GIBCO | 25030081 |
| 2-Mercaptoethanol | Sigma | 6010 |
| Knockout DMEM | GIBCO | 10829018 |
| DMEM:F12 | GIBCO | 11320-033 |
| Neurobasal | GIBCO | 21103-049 |
| IMDM | GIBCO | 31980-030 |
| Fetal Bovine Serum | GIBCO | 26140079 |
| Recombinant Murine IGF-1 | Peprotech | 250-19 |
| Recombinant Human PDGFB | Peprotech | 100-14B |
| Laminin | Sigma | L2020-1MG |
| Klenow, exo- | New England Biolabs | M0212L |
| Critical commercial assays | ||
| NextSeq 500/550 High Output Kit v2.5 (75 Cycles) | Illumina | 20024906 |
| Qubit dsDNA HS Assay kit | Invitrogen | Q32854 |
| QIAquick Gel Extraction Kit | Qiagen | 28706 |
| Qiagen Maxiprep plasmid kit | Qiagen | 12163 |
| Agencourt AMPure XP | Beckman Coulter | A63882 |
| Bioanalyzer D1000 screentapes | Agilent | 5067-5582 |
| LipoD293 | Signagen | SL100668 |
| End-It DNA End-Repair Kit | Biosearch technologies | ER0720 |
| TRIzol™ Reagent | Thermo Fisher | 15596026 |
| EZ DNA Methylation-Lightning Kit | Zymo | D5030 |
| Qiagen DNeasy Blood & Tissue Kit | Qiagen | 69504 |
| Deposited data | ||
| Processed data | GEO | GSE225794 |
| Raw data (Chip-seq) | GEO | GSE225732 |
| Raw data (Capture Bis-seq) | GEO | GSE225793 |
| Experimental models: Cell lines | ||
| mESC (v6.5) | Broad Institute | N/A |
| C57BL/6 MEF 4M IRR | GlobalStem | GSC-6002G |
| Mouse NPCs | This study | N/A |
| Mouse OPCs | This study | N/A |
| 293FT cells | Thermo Fisher | R70007 |
| Human NPCs, BYS012 | ATCC | ACS-5004 |
| Experimental models: Organisms/strains | ||
| 129S1/SvImJ | Jackson laboratories | 002448 |
| Oligonucleotides | ||
| Pdgfra insulator CRISPR locus sequencing: GTCAGGAGTAGATCCTCGTGGCTGAAGACTGGGAGCTATA | IDT | N/A |
| RFX motif CRISPR locus sequencing: TCTCCCTGTTTGGTGCCCTTCTCTCCATCAATCATTGCCAAC | IDT | N/A |
| Cdkn2a-p19 promoter locus bisulfite sequencing: GAAAATTTTTTTTTGGAGTGGGCCTCTAAAAAACTTTCC | IDT | N/A |
| OPC enhancer 4C-seq primers: TGTGGCTTGGCATCCTGATC (viewpoint) TTGAACTCTCAGAGACCCAC | IDT | N/A |
| 18S real time PCR primers: GAGGGAGCCTGAGAAACGG (Forward) GTCGGGAGTGGGTAATTTGC (Reverse) | IDT | N/A |
| Pdgfra real time PCR primers: GACTTCCTAAAGAGTGACCATCC (Forward) CTTCCCAGTCCTTCAGCTTATC (Reverse) | IDT | N/A |
| Cdkn2a real time PCR primers: CATGTTGTTGAGGCTAGAGAGG (Forward) CACCGTAGTTGAGCAGAAGAG (Reverse) | IDT | N/A |
| Recombinant DNA | ||
| pVSV-G | Broad Institute | N/A |
| pCMV delta R8.2 | Broad Institute | N/A |
| CMV-Cas9-T2A-eGFP (lentiviral construct) | This study | N/A |
| U6-ShRNA-U6-sgRNA-CMV-RFP (lentiviral construct) | This study | N/A |
| U6-ShRNA-U6-sgRNA-CMV-RFP-IRES-PDGFB (lentiviral construct) | This study | N/A |
| U6-sgRNA-CMV-Cas9-T2A-eGFP (piggybac construct) | This study | N/A |
| Software and algorithms | ||
| R version 4.1.3 | R Core Team | https://www.r-project.org |
| Benchling (for sgRNA design) | Benchling | https://www.benchling.com |
| ChopChop (for sgRNA design) | ChopChop | https://chopchop.cbu.uib.no |
| Cas off finder (off target analysis) | Cas Off Finder | https://www.rgenome.net/cas-offinder/ |
| Juicer tools | Aiden laboratory | https://github.com/aidenlab/juicer |
| BWA aln version 0.7.4 | Li laboratory | https://github.com/lh3/bwa |
| Picard toolkit 2.9.2 | Broad Institute | https://broadinstitute.github.io/picard/ |
| GVIZ package | Bioconductor | https://bioconductor.org/packages/release/bioc/html/Gviz.html |
| methylCtools 0.9.438 | Hovestadt laboratory | https://github.com/hovestadt/methylCtools |
| MEME suite (version 4.11.3-1) | MEME suite | https://meme-suite.org/meme/doc/download.html |
| LiftOver tool | UCSC genome browser team | https://genome.ucsc.edu/cgi-bin/hgLiftOver |