KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PerCP-Cy5.5-conjugated anti-PAX6 | BD Biosciences | Cat#561462, Clone O18-1330 |
| V450-conjugated anti-SOX2 | BD Biosciences | Cat#561469, Clone O30-678 |
| Alexa Fluor 488-conjugated anti-NeuN | EMD Millipore | Product No. FCMAB317PE, Clone A60 |
| Anti-H3K27ac | Abcam | Prod#ab4729 |
| Anti-H3K4me1 | Abcam | Prod#ab176877 |
| Goat anti-SOX2 (1:200) | Santa Cruz | Cat#sc-170320 |
| Chicken anti-TBR2 (1:200) | Millipore | Cat#AB15894 |
| Rabbit anti-TBR2 (1:200) | Abcam | Prod#ab23345 |
| Rabbit anti-PAX6 (1:200) | Covance | Cat#PRB-278P |
| Mouse anti-HOPX (1:200) | Santa Cruz | Cat. No.. sc-30216 |
| Rabbit anti-PPP1R17 (1:200) | Novus | Cat#NBP2-13800 |
| Mouse anti-PPP1R17 (1:200) | Novus | Cat#H00010842-B01P |
| Mouse anti-SATB2 (1:200) | Abcam | Prod#ab51502 |
| Rabbit anti-Ki67 (1:200) | Abcam | Prod#ab15580 |
| Mouse anti-PCNA | Millipore | Cat#AB93501 |
| Mouse anti-GFAP | Sigma | Cat#G3893 |
| Rat anti-GFAP | Thermo Fisher | Cat#13-0300 |
| Alexa Fluor 488 Anti-Chicken Secondary Antibody | Thermo Fisher | Cat#A11039 |
| Alexa Fluor 594 Anti-Mouse Secondary Antibody | Thermo Fisher | Cat#A11008 |
| Alexa Fluor 594 Anti-Rabbit Secondary Antibody | Thermo Fisher | Cat#A11012 |
| Alexa Fluor 647 Anti-Rat Secondary Antibody | Thermo Fisher | Cat#A21247 |
| DAPI (4′,6-Diamidino-2-Phenylindole, Dihydrochloride) | Thermo Fisher | Cat#D1306 |
| Hoechst 33342 | Thermo Fisher | Cat#62249 |
| Normal Goat Serum | Gibco | Cat#16210064-100ml |
| Bovine Serum Albumin | Sigma | Cat#A7906-100G |
| Fluoromount-G | Southern Biotech | Cat#0100-01 |
| Bacterial and Virus Strains | ||
| One Shot TOP10 Chemically Competent E. coli | Thermo Fisher | Cat#C404006 |
| Biological Samples | ||
| Human brain tissue | This paper | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Formaldehyde | Fisher Scientific | Cat#F79P-4 |
| Glycine | Sigma | Cat#G7126-5KG |
| Triton X-100 | Sigma | Cat#T9284-500ML |
| Paraformaldehyde | Electron Microscopy Sciences | Cat#15710 |
| Fetal bovine serum | Atlanta Bio | Cat#S11150 |
| Dulbecco’s Modified Eagle Medium | Thermo Fisher | Cat#MT10013CV |
| Dulbecco’s Modified Eagle Medium/F12 | Thermo Fisher | Cat#11330032 |
| Penicillin-Streptomycin | Thermo Fisher | Cat#15140122 |
| AMPure XP beads | Beckman-Coulter | Cat#A63881 |
| Retrievagen A | BD Biosciences | Cat#550524 |
| Lysis Buffer | This paper | N/A |
| Wash buffer | This paper | N/A |
| Sonication buffer | This paper | N/A |
| AsiSI restriction enzyme | NEB | Cat#R0630 |
| DNaseI | Sigma-Aldrich | Cat#D4527 |
| MboI | NEB | Cat#R0147 |
| T4 DNA Ligase | Thermo Fisher | Cat#EL0011 |
| Critical Commercial Assays | ||
| Lipofectamine LTX reagent | Thermo Fisher | Cat#A12621 |
| TRIzol reagent | Invitrogen | Cat#15596018 |
| NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina | New England BioLabs | Cat#E6420S |
| Protein A Dynabeads | Thermo Fisher | Cat#10002D |
| Ovation Ultralow V2 kit | Nugen | Cat#0344-32 |
| Neural Tissue Dissociation Kit (T) | Miltenyi Biotec | Cat#130-093-231 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE180714 |
| Human reference genome build GRCh38/hg38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/ |
| Human, chimpanzee, and macaque brain transcriptome data | Sousa et al., 2018 | N/A |
| ENCODE Project and Roadmap Epigenomics Consortium | ENCODE Project Consortium, 2012; Roadmap Epigenomics Consortium et al., 2015 | http://www.roadmapepigenomics.org/ |
| UCSC-tools and genome browser | Kent et al., 2002 | http://genome.ucsc.edu/ |
| Pathway and gene set overdispersion analysis (PAGODA) | Fan et al., 2016 | N/A |
| Single cell ATAC-seq data | Domcke et al., 2020 | https://descartes.brotmanbaty.org/ |
| Experimental Models: Cell Lines | ||
| Neuro2A | ATCC | Cat#CCL-131 |
| SH-SY5Y cell | ATCC | Cat#CRL-2266 |
| Experimental Models: Organisms/Strains | ||
| CD1 Mice | Charles River | Crl:CD1(ICR) |
| Ferrets | Marshall Bioresources | N/A |
| Macaques | Yale University School of Medicine | N/A |
| Oligonucleotides | ||
| CustomArray pool | CustomArray, Bothell, WA | http://www.customarrayinc.com/oligos_main.htm |
| Primers for 3C interaction assay, see Supplemental Data Table S6 | This paper | N/A |
| Recombinant DNA | ||
| Human genomic DNA | Promega | Cat#G1521 |
| Chimpanzee DNA | Coriell | Cat#NS03489 |
| pMPRA1 vector | Melnikov et al., 2014 | Addgene 49349 |
| pMPRA_donor2 | Melnikov et al., 2014 | Addgene 49353 |
| pFucci-G1 Orange | Medical & Biological Laboratories Co., LTD. | Cat#AM-V9003M |
| PBCAG-eGFP | Gift from Joseph LoTurco, Chen et al., 2012 | Addgene 40973 |
| pCyl50 | Gift from Jae Yong Han, Lee et al, 2016 | N/A |
| pCAG-PB-GFP | This paper | N/A |
| pCAG-PPP1R17-PB-GFP | This paper | N/A |
| Software and Algorithms | ||
| MIPgen | Shendure Lab, University of Washington | http://shendurelab.github.io/MIPGEN/ |
| R language | R Core Team, 2019 The R Project for Statistical Computing | https://www.r-project.org/ |
| Python language, version 2.7 | Python Software Foundation | http://www.python.org |
| GraphPad Prism 8 | GraphPad Software Inc., La Jolla, CA, USA | https://www.graphpad.com/scientific-software/prism/ |
| Fiji | Schindelin et al., 2012 | https://imagej.net/ImageJ |
| ImageJ | Schneider et al., 2012 | https://imagej.net/ImageJ |
| IncuCyte Zoom | Essen Bioscience | IncuCyte S3 2018B |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Other | ||
| HARHub | This paper | http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://allendiscoverycenter-harhub.s3.us-east-2.amazonaws.com/HAR_hub/hub.txt |