other:
Recombinant:Article Title: Protocol for a mouse tubuloid model of myoglobinuric acute kidney injury.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins A83-01 Tocris 2939 Advanced DMEM/F-12 Gibco 12634028 B27 supplement Gibco 17504044 Ca 2+ - and Mg 2+ -free PBS Anprotec AC-BS-0002 Collagenase Sigma-Aldrich C4-22 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich D5025-15KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich D4540 Dulbecco’s modified Eagle’s medium High glucose Gibco C11995500BT EGF (murine) Life Technologies AF-315-09-500μg Fetal bovine serum Advanced (FBS) Capricorn FBS-HI-11A FGF-10 (rat) Life Technologies 400-42 Growth factor-reduced Matrigel Corning 354230 HEPES buffer Capricorn HEP-B L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (= Vitamin C) Sigma A8960 Liberase TL Roche 540102001 Myoglobin from equine skeletal muscle Sigma M0630 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Noggin (murine) PeproTech 250-38 Penicillin/Streptomycin Gibco 15140122 Primocin InvivoGen ant-pm-1 Propidium iodide Cayman Chemical Company 14289 Stable glutamine 200 mM Capricorn STA-B Zeocin 500 mg InvivoGen ant-zn-05 Critical commercial assays Qiagen RNeasy Mini Kit Qiagen 74104 Experimental models: Organisms/strains Mouse (Mus musculus): C57BL/6J wild type, male or female, age 9–15 weeks The Jackson Laboratory JAX000664 Experimental models: Primary cells and cell lines Mouse primary renal tubular epithelial cells R-spondin-1-producing HEK293T cells Bio-Techne 3710-001-K R-spondin-1-producing HEK293T cells (alternative) Sigma-Aldrich SCC111 Wnt3a-producing L cells Hubrecht Institute NA; based on MTA Wnt3a-producing L cells (alternative) ATCC CRL-2647 (Continued on next page) 4 STAR Protocols 6, 104205, December 19, 2025 .. Media composition for Wnt3a-producing L cells Media composition for R-spondin-1-producing HEK293T cells Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Hmox1 forward (mouse): 5 ′ -CCTGGTGCAAGATACTGCC-3 ′ Sigma NA Hmox1 reverse (mouse): 5 ′ -GCTCCTTGGTTCTTCCATACAGG-3 ′ Sigma NA Lcn2 forward (mouse): 5 ′ -CTCAGAACTTGATCCCTGCC-3 ′ Sigma NA Lcn2 reverse (mouse): 5 ′ -TCCTTGAGGCCCAGAGACTT-3 ′ Sigma NA Ywhaz forward (mouse): 5 ′ -TTACTTGGCCGAGGTTGCT-3 ′ Sigma NA Ywhaz reverse (mouse): 5 ′ -TGCTGTGACTGGTCCACAAT-3 ′ Sigma NA Software and algorithms GraphPad Prism 10 GraphPad Software Other Bead Ruptor 4 Biolab products 21-25-010 Centrifuge Eppendorf 5810R Ceramic Beads 1.4–1.6 mm Yttrium stabilized Biolab products 21-25-ZY16.5 Circular vibrating shaker Vibramax 100 Heidolph 544-21200-00 Filtropur BT 50, Bottle top filter, 500 ml, 0.22 μm Sarstedt 83.3941.511 μ-Slide 8 well ibidi 80826 Fluorescence microscope Leica Thunder Leica NA MACS smart strainer 70 μm Miltenyi Biotec 130-098-462 Precision scale Mettler AE 200 scale Sonicator Bandelin UW70 Tube roller neoLab CAT RM5 Selection medium Reagent Final concentration Dulbecco’s modified Eagle’s medium high glucose N/A FBS 10% Zeocin 125 μg/ml Store at 4 ◦ C for up to 1 month.
Article Title: Sox9 inhibits Activin A to promote biliary maturation and branching morphogenesis.
Article Snippet: .. After polymerization, Biliary Single Cell Media [50% Advanced DMEM/F12, 40% WNT3A-conditioned media, 10% RSPO1-conditioned media, 2% B27 supplement without vitamin A, 1% N2 supplement, 2mM Glutamax, 10mM HEPES, 100U/mL Pen/Strip, 50 ng/mL recombinant murine EGF (Thermo Fisher; PMG8041), 100 ng/mL recombinant human Noggin (VWR International; 120-10 C), 100 ng/mL recombinant human FGF10 (Peprotech; 100-26), 10 nM recombinant human gastrin (Sigma; G9145), 5 ng/mL recombinant human HGF (PeproTech; 100-39H), 10mM nicotinamide (Sigma Aldrich; N0636-100G), 10 μM forskolin (Selleck Chemicals; S2449), and 10 μM Y-27632]. ..
Article Title: Sox9 inhibits Activin A to promote biliary maturation and branching morphogenesis
Article Snippet: Pellet was visualized by eye, supernatant was discarded, and cells were resuspended in 1 part Advanced DMEM/F12 and 2 parts Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems; 3533-010-02) for a final solution of 66% Cultrex. .. 96 well plates were prewarmed to 37 °C and cell suspensions were plated as 10 μL droplets and allowed to polymerize at 37 °C for 30 min. After polymerization, Biliary Single Cell Media [50% Advanced DMEM/F12, 40% WNT3A-conditioned media, 10% RSPO1-conditioned media, 2% B27 supplement without vitamin A, 1% N2 supplement, 2 mM Glutamax, 10 mM HEPES, 100 U/mL Pen/Strip, 50 ng/mL recombinant murine EGF (Thermo Fisher; PMG8041), 100 ng/mL recombinant human Noggin (VWR International; 120-10 C), 100 ng/mL recombinant human FGF10 (Peprotech; 100-26), 10 nM recombinant human gastrin (Sigma; G9145), 5 ng/mL recombinant human HGF (PeproTech; 100-39H), 10 mM nicotinamide (Sigma Aldrich; N0636-100G), 10 μM forskolin (Selleck Chemicals; S2449), and 10 μM Y-27632]. ..
Article Title: Loss of Paneth cell contact starts a WNT differentiation timer in intestinal crypts
Article Snippet: .. This medium consisted of Advanced DMEM/F-12 462 (Life Technologies) with murine recombinant epidermal growth factor (EGF 50 ng/mL, Life 463 Technologies), murine recombinant Noggin (100 ng/mL, Peprotech), human recombinant R-464 spondin 1 (500 ng/mL, Peprotech), n-Acetylcystein (1 mM, Sigma-Aldrich), N2 supplement (1x, 465 Life Technologies), B27 supplement (1x, Life Technologies), Glutamax (2 mM, Life 466 Technologies), HEPES (10 mM, Life Technologies) and Penicillin/Streptomycin (100 U/mL 100 467 μg/mL, Life Technologies). ..
Modification:Article Title: Protocol for a mouse tubuloid model of myoglobinuric acute kidney injury.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins A83-01 Tocris 2939 Advanced DMEM/F-12 Gibco 12634028 B27 supplement Gibco 17504044 Ca 2+ - and Mg 2+ -free PBS Anprotec AC-BS-0002 Collagenase Sigma-Aldrich C4-22 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich D5025-15KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich D4540 Dulbecco’s modified Eagle’s medium High glucose Gibco C11995500BT EGF (murine) Life Technologies AF-315-09-500μg Fetal bovine serum Advanced (FBS) Capricorn FBS-HI-11A FGF-10 (rat) Life Technologies 400-42 Growth factor-reduced Matrigel Corning 354230 HEPES buffer Capricorn HEP-B L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (= Vitamin C) Sigma A8960 Liberase TL Roche 540102001 Myoglobin from equine skeletal muscle Sigma M0630 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Noggin (murine) PeproTech 250-38 Penicillin/Streptomycin Gibco 15140122 Primocin InvivoGen ant-pm-1 Propidium iodide Cayman Chemical Company 14289 Stable glutamine 200 mM Capricorn STA-B Zeocin 500 mg InvivoGen ant-zn-05 Critical commercial assays Qiagen RNeasy Mini Kit Qiagen 74104 Experimental models: Organisms/strains Mouse (Mus musculus): C57BL/6J wild type, male or female, age 9–15 weeks The Jackson Laboratory JAX000664 Experimental models: Primary cells and cell lines Mouse primary renal tubular epithelial cells R-spondin-1-producing HEK293T cells Bio-Techne 3710-001-K R-spondin-1-producing HEK293T cells (alternative) Sigma-Aldrich SCC111 Wnt3a-producing L cells Hubrecht Institute NA; based on MTA Wnt3a-producing L cells (alternative) ATCC CRL-2647 (Continued on next page) 4 STAR Protocols 6, 104205, December 19, 2025 .. Media composition for Wnt3a-producing L cells Media composition for R-spondin-1-producing HEK293T cells Continued REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Hmox1 forward (mouse): 5 ′ -CCTGGTGCAAGATACTGCC-3 ′ Sigma NA Hmox1 reverse (mouse): 5 ′ -GCTCCTTGGTTCTTCCATACAGG-3 ′ Sigma NA Lcn2 forward (mouse): 5 ′ -CTCAGAACTTGATCCCTGCC-3 ′ Sigma NA Lcn2 reverse (mouse): 5 ′ -TCCTTGAGGCCCAGAGACTT-3 ′ Sigma NA Ywhaz forward (mouse): 5 ′ -TTACTTGGCCGAGGTTGCT-3 ′ Sigma NA Ywhaz reverse (mouse): 5 ′ -TGCTGTGACTGGTCCACAAT-3 ′ Sigma NA Software and algorithms GraphPad Prism 10 GraphPad Software Other Bead Ruptor 4 Biolab products 21-25-010 Centrifuge Eppendorf 5810R Ceramic Beads 1.4–1.6 mm Yttrium stabilized Biolab products 21-25-ZY16.5 Circular vibrating shaker Vibramax 100 Heidolph 544-21200-00 Filtropur BT 50, Bottle top filter, 500 ml, 0.22 μm Sarstedt 83.3941.511 μ-Slide 8 well ibidi 80826 Fluorescence microscope Leica Thunder Leica NA MACS smart strainer 70 μm Miltenyi Biotec 130-098-462 Precision scale Mettler AE 200 scale Sonicator Bandelin UW70 Tube roller neoLab CAT RM5 Selection medium Reagent Final concentration Dulbecco’s modified Eagle’s medium high glucose N/A FBS 10% Zeocin 125 μg/ml Store at 4 ◦ C for up to 1 month.
Single Cell:Article Title: Sox9 inhibits Activin A to promote biliary maturation and branching morphogenesis.
Article Snippet: .. After polymerization, Biliary Single Cell Media [50% Advanced DMEM/F12, 40% WNT3A-conditioned media, 10% RSPO1-conditioned media, 2% B27 supplement without vitamin A, 1% N2 supplement, 2mM Glutamax, 10mM HEPES, 100U/mL Pen/Strip, 50 ng/mL recombinant murine EGF (Thermo Fisher; PMG8041), 100 ng/mL recombinant human Noggin (VWR International; 120-10 C), 100 ng/mL recombinant human FGF10 (Peprotech; 100-26), 10 nM recombinant human gastrin (Sigma; G9145), 5 ng/mL recombinant human HGF (PeproTech; 100-39H), 10mM nicotinamide (Sigma Aldrich; N0636-100G), 10 μM forskolin (Selleck Chemicals; S2449), and 10 μM Y-27632]. ..
Article Title: Sox9 inhibits Activin A to promote biliary maturation and branching morphogenesis
Article Snippet: Pellet was visualized by eye, supernatant was discarded, and cells were resuspended in 1 part Advanced DMEM/F12 and 2 parts Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems; 3533-010-02) for a final solution of 66% Cultrex. .. 96 well plates were prewarmed to 37 °C and cell suspensions were plated as 10 μL droplets and allowed to polymerize at 37 °C for 30 min. After polymerization, Biliary Single Cell Media [50% Advanced DMEM/F12, 40% WNT3A-conditioned media, 10% RSPO1-conditioned media, 2% B27 supplement without vitamin A, 1% N2 supplement, 2 mM Glutamax, 10 mM HEPES, 100 U/mL Pen/Strip, 50 ng/mL recombinant murine EGF (Thermo Fisher; PMG8041), 100 ng/mL recombinant human Noggin (VWR International; 120-10 C), 100 ng/mL recombinant human FGF10 (Peprotech; 100-26), 10 nM recombinant human gastrin (Sigma; G9145), 5 ng/mL recombinant human HGF (PeproTech; 100-39H), 10 mM nicotinamide (Sigma Aldrich; N0636-100G), 10 μM forskolin (Selleck Chemicals; S2449), and 10 μM Y-27632]. ..
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