Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Stbl3 Chemically Competent E. coli | Invitrogen | Cat# C737303 |
| Chemicals, peptides, and recombinant proteins | ||
| Agencourt AMPure Beads | Beckman | Cat# A63881 |
| DNase-I | New England Biolabs | Cat# M0303S |
| EcoRI | New England Biolabs | Cat# R3101S |
| Fast Green FCF | Sigma-Aldrich | Cat# F7252 |
| FBS | ThermoFisher | Cat# 10438026 |
| Hoechst 33342 | Invitrogen | Cat# H1399 |
| NEG-50 | Richard-Allan Scientific | Epredia 6502 |
| Phusion DNA Polymerase | New England Biolabs | Cat# M0530S |
| SphI | New England Biolabs | Cat# R3182S |
| Trypsin-EDTA | Sigma-Aldrich | Cat# 59428C |
| Vectashield | Vector Laboratories | H-1000-10 |
| ZymoPURE II Plasmid Maxiprep Kit | Zymo Research | Cat# D4203 |
| Critical commercial assays | ||
| LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit | Invitrogen | Cat# L10119 |
| NovaSeq 6000 S-Prime Reagents | Illumina | Cat# 20040719 |
| Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 | 10x Genomics | https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry |
| NEBuilder HiFi DNA Assembly Master Mix | New England Biolabs | Cat# E2621L |
| NEBNext Ultra II FS DNA Library Prep Kit | New England Biolabs | Cat# E6177 |
| Deposited data | ||
| 1000 Genomes Project genomes | Byrska-Bishop et al. (2022) | https://www.internationalgenome.org/data-portal/data-collection/30x-grch38 |
| Altai Neanderthal genome | Meyer et al. (2012) | https://www.eva.mpg.de/genetics/genome-projects/neandertal/ |
| Combined Human Accelerated Region locations | Doan et al. (2016) | Table S1 of Doan et al. (2016) |
| Denisovan genome | Meyer et al. (2012) | https://www.eva.mpg.de/denisova/index.html |
| ENCODE cCRE locations and ChromHmm Datasets | Moore et al. (2020) | https://www.encodeproject.org/ |
| GWAS Catalog Variants | GWAS Catalog | https://www.ebi.ac.uk/gwas/ |
| HiCAR H1 and GM12878 | Wei et al. (2022) | GEO: GSE162819 |
| Human ChromHmm Roadmap Epigenomics data | Kundaje et al. (2015) | http://www.roadmapepigenomics.org/ |
| Human gained enhancer locations | Reilly et al. (2015) | GEO: GSE63648 |
| Individual chimpanzee genomes | Prado-Martinez et al. (2013) | https://www.ncbi.nlm.nih.gov/sra?term=SRP018689 |
| knownGene | Navarro Gonzalez et al. (2021) | https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ |
| Meiotic Recombination DSB hotspots | Pratto et al. (2014) | GEO: GSE59836 |
| Raw and processed sequencing reads | This study | GEO: GSE212159 |
| Recombination frequency maps | Zhou et al. (2020) |
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/2013050 7 omnirecombination rates/ |
| Reference genomes: hg38, panTro6, panPan2, gorGor5, gorGor6, ponAbe3 | UCSC Genome Browser | https://hgdownload.soe.ucsc.edu/downloads.html |
| Replication timing datasets | Ding et al. (2021) | https://www.thekorenlab.org/data |
| Ultraconserved Element locations | Bejerano et al. (2004) | https://hgwdev.gi.ucsc.edu/ |
| Vindija Cave Neanderthal genome | Prüfer et al. (2017) | https://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J (B6) (WT) | The Jackson Laboratory | JAX: 000664 |
| Oligonucleotides | ||
| Synthetic STARR-seq Insert Sequences | This study | Supplemental Dataset 1 |
| Targeted Enrichment Primers | This study | Supplemental Dataset 1 |
| Recombinant DNA | ||
| hSTARR-seq ORI vector | Addgene | RRID: Addgene 99296 |
| PGK-EGFP | Addgene | RRID: Addgene 169744 |
| Software and algorithms | ||
| bcl2fastq2 Conversion Software v2.20 | Illumina | https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html |
| BWA 0.7.17 | Li and Durbin (2009) | https://github.com/lh3/bwa |
| CellRanger v6.0 | 10x Genomics | https://support.10xgenomics.com/ |
| ClustalW2 | (Larkin et al., 2007) | https://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/ |
| gonomics | Vertebrate Genetics Laboratory | https://github.com/vertgenlab/gonomics |
| GraphPad Prism | GraphPad | https://www.graphpad.com/ |
| GREAT version 4.0.4 | McLean et al. (2010) | http://great.stanford.edu/public/html/ |
| ImageJ | Schindelin et al. (2012) | https://imagej.nih.gov/fiij/ |
| kentUtils | Kent et al. (2003) | https://github.com/ENCODE-DCC/kentUtils |
| lastz | Harris (2007) | https://github.com/lastz/lastz |
| multiz | Blanchette et al. (2004) | https://bio.tools/multiz |
| muscle | Edgar (2004) | https://www.ebi.ac.uk/Tools/msa/muscle/ |
| phylotree | Shank et al. (2018) | https://phylotree.hyphy.org/ |
| Plink | Purcell et al. (2007) | https://zzz.bwh.harvard.edu/plink/ |
| R version 4.0.5 | R Foundation for Statistical Computing | https://www.r-project.org/ |
| RPHAST | Hubisz et al. (2011) | https://github.com/CshlSiepelLab/RPHAST |
| Seurat v4.0 | Hao et al. (2021) | https://satijalab.org/seurat/ |
| SNPeff | Cingolani et al. (2012) | http://pcingola.github.io/SnpEff/ |