KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-POU5F1 | Santa Cruz | Sc-5279; RRID: AB_628051 |
| Anti-T (Brachyury) (APC-conjugated) | R&D Systems | IC2085A; RRID: AB_2271455 |
| Anti-TBX6 | R&D Systems | AF4744; RRID: AB_2200834 |
| Anti-MEOX1 | Atlas Antibodies | HPA045214; RRID: AB_10959299 |
| Chicken anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | A-21201; RRID: AB_2535787 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 350 | Thermo Fisher Scientific | A-21081; RRID: AB_2535738 |
| Chicken anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | A-21441; RRID: AB_2535859 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| CHIR 99021 | Tocris | 4423 |
| A 83-01 | Tocris | 2939 |
| DAPT | Tocris | 2634 |
| endo-IWR1 | Tocris | 3532 |
| XAV 939 | Tocris | 3748 |
| (+)-JQ1 | Tocris | 4499 |
| 10058-F4 | Tocris | 4406 |
| Y-27632 dihydrochloride | Tocris | 1254 |
| RepSox | Tocris | 3742 |
| SB 431542 | Tocris | 1614 |
| Recombinant Human Noggin Protein | R&D Systems | 6057-NG-01M/CF |
| Recombinant Human TGF-beta 1 Protein, CF | R&D Systems | 240-B/CF |
| Human Holo-Transferrin Protein, CF | R&D Systems | 2914-HT |
| Porcn Inhibitor II, C59 | Sigma-Aldrich | 5004960001 |
| Insulin solution human | Sigma-Aldrich | I9278 |
| Doxycycline hyclate | Sigma-Aldrich | D9891 |
| BD Matrigel Matrix Growth Factor Reduced | BD Biosciences | 354230 |
| UltraPure 0.5M EDTA, pH 8.0 | Thermo Fisher Scientific | 15575020 |
| Dulbecco’s phosphate-buffered saline (DPBS) | Thermo Fisher Scientific | 14190250 |
| DMEM/F-12 | Thermo Fisher Scientific | 11320082 |
| StemPro Accutase Cell Dissociation Reagent | Thermo Fisher Scientific | A1110501 |
| TrueCut Cas9 Protein v2 | Thermo Fisher Scientific | A36497 |
| Critical Commercial Assays | ||
| GeneArt Precision gRNA Synthesis Kit | Thermo Fisher Scientific | A29377 |
| GeneArt Genomic Cleavage Detection Kit | Thermo Fisher Scientific | A24372 |
| POU5F1 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00999634_gH |
| TBX6 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00365539_m1 |
| HES7 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs03988571_m1 |
| LFNG TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00385436_g1 |
| DLL1 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00194509_m1 |
| MEOX1 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00244943_m1 |
| FOXC2 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs00270951_s1 |
| MSGN1 TaqMan Assay (4331182) | Thermo Fisher Scientific | Hs03405514_s1 |
| GAPDH TaqMan Assay (VIC_PL, 4448486) | Thermo Fisher Scientific | Hs02786624_g1 |
| Nano-Glo(R) Live Cell EX-6829 | Promega | CS2025A03 |
| Deposited Data | ||
| Raw RNA-seq data | This paper | GEO: GSE128469 |
| Experimental Models: Cell Lines | ||
| Human: WA01 (H1) hESC line (NIH approval number NIHhESC-10-0043) | WiCell | WA01: H1 Human ES |
| Oligonucleotides | ||
| HES7 knockin junction PCR, in Table S2 | This paper | Synthesized from IDT |
| HES7 for Southern blotting probe template, in Table S2 | This paper | Synthesized from IDT |
| Primers for make HES7-C73T-gRNA template, in Table S2 | This paper | Synthesized from IDT |
| Oligo for HES7-C73T-ssODN donor, in Table S2 | This paper | Synthesized from IDT |
| Primers for sequencing HES7 Exon2, in Table S2 | This paper | Synthesized from IDT |
| Recombinant DNA | ||
| HES7-NLuc-2A-tdTomato knockin vector | This paper | Addgene, 130932 |
| pCRII-Blunt-U6-HES7-STOP-gRNA | This paper | Addgene, 130933 |
| pB-TAG-NICD | This paper | Addgene, 130934 |
| pB-TAG-HES7 | This paper | Addgene, 130935 |
| pB-EF1a-NLuc | This paper | Addgene, 130936 |
| NanoLuc gene cassette | Promega | GeneBank: JQ437370 |
| Software and Algorithms | ||
| Bandpass and detrending Perl code | This paper | https://github.com/stewart-lab/Detrending |
| Wave-Crest | Chu et al., 2016 | https://github.com/lengning/WaveCrest |
| Trendy | Bacher et al., 2018 | https://rbacher.shinyapps.io/trendy/ |
| Enrichr | Chen et al., 2013 | http://amp.pharm.mssm.edu/Enrichr/ |
| Other | ||
| scRNA-seq data for somitomere cells | Loh et al., 2016 | http://imlspenticton.uzh.ch:3838/conquer/ |