Reagents used in this study.

SourceProduct ID
Cell lines
 C57BL/6J × CAST mESCsFrom: Sun et al (2012)N/A
 CAST × C57BL/6J mESCsFrom: Sun et al (2012)N/A
 129 × C57BL/6 mESCsFrom: Mohn et al (2008)N/A
Chemicals, peptides, and recombinant proteins
 DMEMGibco21969-035
 Nonessential amino acidsGibco11140035
 100 mM Sodium pyruvateGibco11360070
 200 mM l-glutamineGibco25030024
 FBSGibco10270106
 β-MercaptoethanolSigma-AldrichM-7522
 GelatinSigma-AldrichG-1890
 Trypsin–EDTAGibco25300-054
 Dulbecco’s PBSGibco14190
 Trypsin (TPCK-treated)Sigma-AldrichT8802
 Retinoic acidSigma-AldrichR-2625
 GSK3 inhibitor CHIR99021Calbiochem361559
 MEK inhibitor PD 0325901Tocris4192
 NDiff227 mediumStem CellsSCS-SF-NB-02
 OptiMEMGibco31985070
 Lipofectamine 3000 Transfection kitInvitrogenL3000015
 cOmplete Protease Inhibitor CocktailRoche11836145001
 Proteinase KRoche3115879001
 SuperScript IIILife Technologies18080085
 Anti-FLAG M2 magnetic beadsSigma-AldrichM8823
 3× FLAG peptideSigma-AldrichF4799-25MG
 Dynabead M-280 StreptavidinInvitrogen11206D
 RNace-It Ribonuclease CocktailAgilent400720
 TSAP Thermosensitive Alkaline PhosphatasePromegaM9910
 RNasin Ribonuclease InhibitorPromegaN2115
 Recombinant RNasin Ribonuclease InhibitorPromegaN2511
 miR-cat 33 conversion oligo packIDTCustom order
 T4 RNA Ligase 1 (ssRNA Ligase)NEBM0204L
 T4 PNK, T4 polynucleotide kinaseNEBM0201L
 Hybond-C Extra membraneGE HealthcareRPN303E
 Kodak BioMax MS autoradiography filmKodak8222648
 MetaPhor agaroseLonza50180
 NuPAGE 4–12% (wt/vol) polyacrylamide Bis-Tris gelsLife TechnologiesNP0335
 NuPAGE LDS sample buffer 4×Life TechnologiesNP0007
 NuPAGE SDS-MOPS running bufferLife TechnologiesNP0001
 NuPage transfer bufferLife TechnologiesNP00061
 MinElute Gel Extraction kitQiagen28604
 Proteinase KRoche03115836001
 RNase HNEBM0297L
 TaKaRa long and accurate (LA) TaqClontechRR002M
 γ32P-ATP 0.5 mCi 18.5 MBq Spec act. >6,000 Ci/mmolHartmanSRP-501
 RCC RNA Spike-In Mix 1Ambion4456740
 Single Cell RNA Purification kitNorgen51800
Recombinant DNA
 SpCas9-sgRNA-2A-mCherryKnuckles et al (2017)
 pRRE200 homologous recombination reporterFlemr & Buhler (2015)
 pRRP200 homologous recombination reporterFlemr & Buhler (2015)
 pBluescript II KS(–)Stratagene
 psiCHECK-2PromegaC8021
 Oligonucleotides are listed in Table S5IDT