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2011 addgene plasmid 44012 software  (Addgene inc)


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    Addgene inc 2011 addgene plasmid 44012 software
    2011 Addgene Plasmid 44012 Software, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 372 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/2011+addgene+plasmid+44012+software/pInducer20+(Plasmid+%2344012)/pm30244869-237-152-153
    Average 96 stars, based on 372 article reviews
    2011 addgene plasmid 44012 software - by Bioz Stars, 2026-09
    96/100 stars

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    Related Articles

    Synthesized:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..

    Control:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..

    Quantitative RT-PCR:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..

    Recombinant:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..

    Plasmid Preparation:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..

    Software:

    Article Title: Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Activin A Cell Guidance Systems Cat#GFH6 CHIR99021 Stemgent Cat#04-0004 BIO Tocris Cat#3194 Y-27632 dihydrochloride Tocris Cat#1254 SB431542 Tocris Cat#1614 Doxycycline Sigma-Aldrich Cat#D3447 Tamoxifen Sigma-Aldrich Cat#T5648 hESC-qualified Matrigel BD Biosciences Cat#354277 mTeSR1 media Stem Cell Technologies Cat#5850 Advanced DMEM:F12 Thermo Fisher Scientfic Cat#12634-010 Matrigel BD Biosciences Cat#354234 Defined fetal bovine serum (dFBS) Hyclone Cat#SH30070.02 Proteinase K Thermo Fisher Scientifc Cat#AM2548 Normal donkey serum Jackson Immunoresearch Labs Cat#017-000-121 Heat-inactivated lamb serum GIBCO Cat#16070096 Blocking Reagent Sigma-Aldrich Cat#11096176001 L-glutamine (100x) Thermo Fisher Scientific Cat#25030-081 Pen/Strep (100x) Thermo Fisher Scientific Cat#15140-122 50x B27 supplement w/o Vitamin A Thermo Fisher Scientific Cat#12587-010 Non-essential Amino Acids (100x) Thermo Fisher Scientific Cat#11140050 HEPES Buffer Thermo Fisher Scientific Cat#15630080 N2 Supplement Thermo Fisher Scientific Cat#17502-048 Dispase Thermo Fisher Scientific Cat#17105-041 Acutase Thermo Fisher Scientific Cat#A11105-01 Collagen Type I, rat tail EMD Millipore Cat#08-115 Transwell 24mm Polyester Membrane Inserts, 6 well plate Corning Cat#3450 Deep Well Plate, 6 well BD Cat#355467 Ahlstrom Filter Papers – Grade 222 Fisher Scientific Cat#09-790-49J 1,2-Dioctanoyl-sn-glycerol Cayman Chemicals Cat#62225 F12 Media Invitrogen Cat#11765-054 1x DMEM Invitrogen Cat#11965-084 Fetal Bovine Serum (FBS) HyClone Cat#SH30071.03 Adenine Sigma-Aldrich Cat#A2786-5G Cholera toxin EMD Millipore Cat#227035 Hydrocortisone Sigma-Aldrich Cat#H0888-1G Fungizone (Amphotericin B) Omega Scientific Cat#FG-70 Insulin, human recombinant Invitrogen Cat#12585-014 EGF Sigma-Aldrich Cat#1257-0.1MG RNAlater Thermo Fisher Scientific Cat#AM7020 Critical Commercial Assays Quantitect SYBR Green QIAGEN Cat#204145 Nucleospin RNA Macherey-Nagel Cat#740955 SuperScript VILO cDNA synthesis kit Thermo Fisher Scientific Cat#11754250 Click-iT EdU Alexa Fluor 488 Imaging Kit Invitrogen Cat#C10337 Deposited Data Raw and analyzed RNA-seq data This paper GSE112886 (Continued on next page) Cell Stem Cell 23, 501–515.e1–e7, October 4, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines Human: H1 ES cells (passage 42) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0043 Human: H9 ES cells (passage 30) CCHMC Pluripotent Stem cell core / WiCell Research Institute NIH hESC-10-0062 Human: iPS65.8 iPS cells (passage 44) CCHMC Pluripotent Stem cell core N/A Human: iPS72.3 iPS cells (passage 35) CCHMC Pluripotent Stem cell core N/A Human: iPS263.10 iPS cells (passage 30) N/A N/A Human: WTC CRISPRi-SOX2 iPS cells (passage 43) Conklin lab Mandegar et al., 2016 Experimental Models: Organisms/Strains Mouse: Foxa2tm2.1(cre/Esr1*)Moon/J The Jackson Laboratory JAX: 008464 Mouse: B6;129S-Sox2tm1(cre/ERT2)Hoch/J The Jackson Laboratory JAX: 017593 Mouse: Sox2tm1.1Lan/J Lang Lab (JAX: 013093) Xenopus laevis N/A N/A Oligonucleotides sox2- UTR MO: CTGGCAGAGCGGAATCAGTTTCCCA GeneTools N/A (synthesized) sox2- ATG MO: AGCTCGGTCTCCATCATGCTGTAC GeneTools N/A (synthesized) control MO: CCTCTTACCTCAGTTACAATTTATA GeneTools N/A (synthesized) See Table S1 for qRT-PCR primers IDT DNA N/A (synthesized) Recombinant DNA pINDUCER20 Meerbrey et al., 2011 Addgene plasmid 44012 Software and Algorithms Imaris Bitplane N/A NIS Elements Nikon N/A Computational Suite for Bioinformaticians and Biologists version 2.1 (CSBB v2.1) N/A https://sourceforge.net/projects/ csbb-v2-1/ Gene Set Enrichment Analysis (GSEA) N/A Subramanian et al., 2005 PRISMv6 graphing and statistical software GraphPad Software N/A ..



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