KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FOS antibody [2H2] | Abcam | Cat # AB208942; RRID: AB_2747772 |
| Anti-MAP2 | Abcam | Cat #ab5392; RRID: AB_2138153 |
| Anti-H3K27ac | Abcam | Cat # AB4729; RRID: AB_2118291 |
| Anti-IgG | Abcam | Cat # AB46540; RRID: AB_2614925 |
| Anti-IgG | Novus | Cat # NBP1-2763 |
| Anti-HSP90 | Cell Signaling | Cat # 4874S; RRID: AB_2121214 |
| Anti-FOS | Abcam | Cat # AB208942; RRID: AB_2747772 |
| Anti-pERK1/2 | Cell Signaling | Cat # 9101S; RRID: AB_331646 |
| Anti-Dlx5 | Wang et al., 2010 | Made and kindly shared by John LR Rubenstein’s group. |
| Anti-Dlx2 | Santa Cruz Biotechnology, Inc | Cat # sc-393879 |
| Chemicals, peptides, and recombinant proteins | ||
| Stemflex supplement | Gibco | Cat # A33492 |
| Stemflex basal media | Gibco | Cat # A33493-01 |
| Geltrex | Gibco | Cat # A14133-02 |
| Poly-L-ornithine hydrobromide | Sigma | Ct # P3655 |
| Accutase | Thermo Scientific | Cat # NC9464543 |
| Thiazovivin | Santa Cruz | Cat # SC-361380 |
| Puromycin dihydrochloride from Streptomyces alboniger | Sigma | Cat # P8833 |
| Hygromycin B (50 mg/mL) | Life Technologies | Cat # 10687010 |
| Cytosine β-D-arabinofuranoside hydrochloride | Sigma | Cat # C1768 |
| TRIzol | Invitrogen | Cat # 15596026 |
| Tetrodotoxin citrate (TTX) | Labome | Cat # 1069/1 |
| DL-2-amino-5-phosphopentnoic acid (DL2-AP5) | Abcam | Cat # ab120271 |
| DMEM media | Gibco | Cat # 11965-092 |
| MEM NEAA (100x) | Gibco | Cat # 11140-050 |
| Sodium Pyruvate (100x) | Gibco | Cat # 11360-070 |
| β-Mercaptoethanol | Sigma | Cat # M3148 |
| Cytiva HyClone™ Cosmic Calf™ Serum | Fisher | Cat # SH3008704 |
| Fetal Bovine Serum (FBS) | Sigma | Cat # F6178 |
| Doxycycline | Sigma | Cat # P3655 |
| MEM media | Gibco | Cat # 11090-081 |
| Glutamax (100×) | Gibco | Cat # 35050-061 |
| B27 supplement | Gibco | Cat # 17504-044 |
| Neurobasal media | Gibco | Cat # 21103-049 |
| Naurobasal A media | Gibco | Cat # 10888-022 |
| Trypsin 0.25% | Gibco | Cat # 25200-114 |
| DMEM/F12 media | Gibco | Cat # 11320-033 |
| N2 supplement | Gibco | Cat # 17502-048 |
| Dimethyl sulfoxide | Sigma | Cat # D2438 |
| Paraformaldehyde solution | Affymetrix | Cat # 19943 |
| D-PBS tablets | Millipore | Cat # 524650-1EA |
| Protease Free Heat Shock Bovine Serum Albumin Powder | Equitech-Bio | Cat # BAH65-0500 |
| Urea | Sigma | Cat # U5128 |
| 1M HEPES/Sodium Hydroxide | Rigaku | Cat # 1008184 |
| RNase A | Thermo Fisher Scientific | Cat #EN0531 |
| Glycogen | Sigma | Cat #10930193001 |
| Spermidine | Sigma | Cat # S0266 |
| cOmplete™, EDTA-free Protease Inhibitor Cocktail | Sigma/Roche | Cat # 11873580001 |
| Concanavalin A (ConA)-coated magnetic beads | Bangs Laboratories | Cat # BP531 |
| Protein AG-MNase | EpiCypher | Cat # 15-1116 |
| AMPure XP beads | Beckman Coulter | Cat # A63881 |
| SYBR green 2x master mix | Applied Biosystems | Cat # 4367659 |
| Critical commercial assays | ||
| Tagment DNA Enzyme and Buffer kit | Illumina | Cat # 20034211 |
| MinElute Reaction Cleanup Kit | Qiagen | Cat # 28206 |
| NEB Next High-Fidelity 2x PCR Master Mix | New England Biolabs | Cat # M0541 |
| Pierce™ BCA Protein Assay Kit | Thermo Scientific | Cat # 23225 |
| TURBO™ DNase | Ambion | Cat # AM1907 |
| SuperScript® IV First-Strand Synthesis System | Thermo Scientific | Cat # 18091050 |
| Bolt™ 4 to 12%, Bis-Tris, 1.0 mm, Mini Protein Gel, 15-well | Thermo Scientific | Cat # MW04125BOX |
| iBlot™ 2 Transfer Stacks, PVDF | Invitrogen | Cat # IB24001 |
| Western Lightning Plus, Chemiluminescent Substrate | Perkin Elmer | Cat # NEL 104001EA |
| NEBNext Ultra II DNA library Prep kit for Ilumina | New England Biolabs | Cat # E7645 |
| NEBNext Multiplex oligos for Ilumina | New England Biolabs | Cat # E7600S and Cat # E7780S |
| Deposited Data | ||
| Raw RNA-sequencing data and Salmon counts | This paper | GEO: GSE196855 |
| Raw ATAC-sequencing data and processed peaks | This paper | GEO: GSE196854 |
| Raw H3K27ac CUT&RUN data and processed peaks | This paper | GEO: GSE196207 |
| Experimental models: cell lines | ||
| H1 (WA01) | WiCell Research Resources | hPSC Reg ID Ae001-A |
| 3188-2A-4N | Hoffman et al., 2017 | GEO: GSM2843584 |
| HEK293T | ATCC | Cat # 11268 |
| Experimental models: organisms/strains | ||
| CD1 mouse strain | Charles River | Cat# CRL:022, RRID: IMSR_CRL:022 |
| Recombinant DNA | ||
| FUW-M2rtTA | Hockemeyer et al., 2008 | RRID: Addgene_20342 |
| TetO-Ascl1-puro | Yang et al., 2017 | RRID: Addgene_97329 |
| TetO-Ngn2-puro | Zhang et al., 2013 | RRID: Addgene_52,047 |
| TeoO-Dlx2-Hygro | Yang et al. 2017 | RRID: Addgene_97330 |
| Software and algorithms | ||
| Bowtie2 | Langmead and Salzberg, 2012 | RRID: SCR_016368; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Skewer v0.2.2 | Jiang et al., 2014 | https://github.com/relipmoc/skewer |
| Salmon 0.13.1 | Patro et al., 2017 | https://combine-lab.github.io/salmon/ |
| R | Love et al., 2014 | https://www.r-project.org/ |
| RStudio | RStudio Team, 2020 | https://github.com/rstudio/ |
| Apeglm | Zhu et al., 2019 | https://github.com/azhu513/apeglm |
| ENCODE ATAC-seq pipeline v1.4.2 | Consortium, 2012 | https://www.encodeproject.org/atac-seq/ |
| featureCounts | http://subread.sourceforge.net/ | |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Trimmomatic | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| MACS | Zhang et al., 2008 | https://github.com/macs3-project/MACS |
| DiffBind | Stark and Brown, 2011 | http://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| ChipSeeker | Yu et al., 2015 | https://guangchuangyu.github.io/software/ChIPseeker/ |
| LDSC | Finucane et al., 2015 | https://github.com/bulik/ldsc |
| Prism | GraphPad | RRID: SCR_005375 |