Reagents used in this study.
| Source | Product ID | |
| Cell lines | ||
| C57BL/6J × CAST mESCs | From: Sun et al (2012) | N/A |
| CAST × C57BL/6J mESCs | From: Sun et al (2012) | N/A |
| 129 × C57BL/6 mESCs | From: Mohn et al (2008) | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM | Gibco | 21969-035 |
| Nonessential amino acids | Gibco | 11140035 |
| 100 mM Sodium pyruvate | Gibco | 11360070 |
| 200 mM l-glutamine | Gibco | 25030024 |
| FBS | Gibco | 10270106 |
| β-Mercaptoethanol | Sigma-Aldrich | M-7522 |
| Gelatin | Sigma-Aldrich | G-1890 |
| Trypsin–EDTA | Gibco | 25300-054 |
| Dulbecco’s PBS | Gibco | 14190 |
| Trypsin (TPCK-treated) | Sigma-Aldrich | T8802 |
| Retinoic acid | Sigma-Aldrich | R-2625 |
| GSK3 inhibitor CHIR99021 | Calbiochem | 361559 |
| MEK inhibitor PD 0325901 | Tocris | 4192 |
| NDiff227 medium | Stem Cells | SCS-SF-NB-02 |
| OptiMEM | Gibco | 31985070 |
| Lipofectamine 3000 Transfection kit | Invitrogen | L3000015 |
| cOmplete Protease Inhibitor Cocktail | Roche | 11836145001 |
| Proteinase K | Roche | 3115879001 |
| SuperScript III | Life Technologies | 18080085 |
| Anti-FLAG M2 magnetic beads | Sigma-Aldrich | M8823 |
| 3× FLAG peptide | Sigma-Aldrich | F4799-25MG |
| Dynabead M-280 Streptavidin | Invitrogen | 11206D |
| RNace-It Ribonuclease Cocktail | Agilent | 400720 |
| TSAP Thermosensitive Alkaline Phosphatase | Promega | M9910 |
| RNasin Ribonuclease Inhibitor | Promega | N2115 |
| Recombinant RNasin Ribonuclease Inhibitor | Promega | N2511 |
| miR-cat 33 conversion oligo pack | IDT | Custom order |
| T4 RNA Ligase 1 (ssRNA Ligase) | NEB | M0204L |
| T4 PNK, T4 polynucleotide kinase | NEB | M0201L |
| Hybond-C Extra membrane | GE Healthcare | RPN303E |
| Kodak BioMax MS autoradiography film | Kodak | 8222648 |
| MetaPhor agarose | Lonza | 50180 |
| NuPAGE 4–12% (wt/vol) polyacrylamide Bis-Tris gels | Life Technologies | NP0335 |
| NuPAGE LDS sample buffer 4× | Life Technologies | NP0007 |
| NuPAGE SDS-MOPS running buffer | Life Technologies | NP0001 |
| NuPage transfer buffer | Life Technologies | NP00061 |
| MinElute Gel Extraction kit | Qiagen | 28604 |
| Proteinase K | Roche | 03115836001 |
| RNase H | NEB | M0297L |
| TaKaRa long and accurate (LA) Taq | Clontech | RR002M |
| γ32P-ATP 0.5 mCi 18.5 MBq Spec act. >6,000 Ci/mmol | Hartman | SRP-501 |
| RCC RNA Spike-In Mix 1 | Ambion | 4456740 |
| Single Cell RNA Purification kit | Norgen | 51800 |
| Recombinant DNA | ||
| SpCas9-sgRNA-2A-mCherry | Knuckles et al (2017) | |
| pRRE200 homologous recombination reporter | Flemr & Buhler (2015) | |
| pRRP200 homologous recombination reporter | Flemr & Buhler (2015) | |
| pBluescript II KS(–) | Stratagene | |
| psiCHECK-2 | Promega | C8021 |
| Oligonucleotides are listed in Table S5 | IDT |