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130933 pb tag nicd  (Addgene inc)


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    Addgene inc 130933 pb tag nicd
    130933 Pb Tag Nicd, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/130933+pb+tag+nicd/pCRII-Blunt-U6-HES7-STOP-gRNA+(Plasmid+%23130933)/pm31461642-138-132-136
    Average 90 stars, based on 1 article reviews
    130933 pb tag nicd - by Bioz Stars, 2026-09
    90/100 stars

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    TaqMan Assay:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    RNA Sequencing:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Knock-In:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Polymerase Chain Reaction:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Synthesized:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Southern Blot:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Sequencing:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Recombinant:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..

    Software:

    Article Title: An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells
    Article Snippet: 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 (Continued on next page) e1 Cell Reports 28, 2247–2255.e1–e5, August 27, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 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/ ..



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