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8 protocols using ampicillin

1

Lgr5+ Cell Sphere Formation and Differentiation

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The cells sorted by FAC were cultured in DMEM/F12 medium supplemented with N2 (1%, Invitrogen), B27 (2% dilution, Invitrogen), EGF (20 ng/ml, Sigma), bFGF (10 ng/ml, Sigma), and IGF-1 (50 ng/ml, Sigma), heparin sulfate (50 ng/ml, Sigma) (full medium), and ampicillin (0.1%, Beyotime). For sphere-forming assay, the sorted cells were seeded on TCPS or graphene substrates with 200 cells per well for 5 days. Subsequently, we measured the number and diameter of the formed spheres to evaluate their proliferation capacity. For differentiation assay, the sorted single cells and formed spheres were differentiated separately. The cells or spheres were cultured in a 4-well dish for 10 days, and immunofluorescence staining was then applied to analyze the differentiation of Lgr5+ cells. As described in previous reports, cell aggregation with more than 5 cells were considered a sphere or colony.
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2

Cochlear Basilar Membrane Isolation and Treatment

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The cochleae of P3 wild-type mice were dissected from the inner ear and immersed in bioclean HBSS (Multicell, 311512011) using a stereo microscope. The spiral ganglion, spiral ligament, and stria vascularis of cochleae were removed, and the cochlear basilar membranes were put in dishes that were smeared with Corning® Cell-Tak™ and then cultured with DMEM-F12 medium added with ampicillin (Beyotime, ST008), N2 Supplement (Stemcell, 07152), and SM1 neuronal supplement (Stemcell, 05711) for 12 h in an incubator at 37°C, 5% CO2. About 0.01 μm PTV was given to the samples for 12 h, and then, 0.5 mm neomycin with 0.01 μm PTV was given together to the cochleae for another 12 h.
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3

Isolating and Culturing Mouse Kölliker's Organ

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For these experiments, we used pups from the same litter which was reserved for their tails for genotype identification during the experiment.
Kölliker’s organ was micro-dissected in cold 1× Hank’s balanced salt solution (HBSS, Thermo Fisher, 14025076, USA) as described above, transiently transferred to an Eppendorf tube containing DMEM/F12 mixed with 2% ampicillin (ST008, Beyotime, China) and then cultured as previously reported (Chen et al., 2018 (link)). Briefly, Kölliker’s organ was divided into three fragments from apex to base and the fragments were placed in a 24-well plate containing a tissue culture-treated, round glass slide (14 mm diameter, WHB-24-CS, WHB) immersed in DMEM/F12 containing 1% ampicillin, 10% fetal bovine serum (10099-141, Gibco, Australia). Alternatively, for Ca2+ imaging experiments with fluo-4 (see below), Kölliker’s organ fragments were placed on a tissue culture-treated glass-bottomed culture dish (801001, NEST, China). In either case, the culture medium was supplemented with 10 μM (Z)-4-hydroxytamoxifen (H7904, Sigma, Germany) to promote Cre recombinase-mediated in vitro excision of the floxed Cx26 alleles. Finally, samples were placed in an incubator (Thermo Scientific Forma Direct Heat CO2 Incubators) and cultured at 37°C, 5% CO2 for 12 h (Chen et al., 2018 (link)).
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4

Site-Directed Mutagenesis of MafA Constructs

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Each construct of MafA with single lysine (K) to arginine (R) mutation was generated by using a PCR-based site-directed mutagenesis under direction of TransStart Fast pfu DNA polymerase (TransGen) as described previously (20 (link)) by mutating lysine codes (AAA or AAG) to arginine codes (AGA or AGG) where it was applicable. At the end of the PCR, the reactions were treated for 30 min by DpnI (Thermo Fisher Scientific), followed by transformation into DH5α competent cells (TIANGEN) and cultured in LB agar plates containing ampicillin (Beyotime).
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5

Methylation Analysis of SH2D5 Promoter

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MethPrimer online software (http://www.urogene.org/methprimer/) was used to obtain information of the CpG island of the SH2D5 gene promoter region and to design methylation-specific PCR (MSP) primers. The genomic DNA was extracted, treated with an EZ DNA Methylation-Direct Kit (Tiangen Biotech Co., Ltd.), and purified. Each MSP reaction consisted of 1 μL of vulcanized DNA as a template, 1 μL of upstream and downstream primers, 1.6 μL of dNTPs (2.5 nM), 0.4 μL of MSP DNA polymerase (2.5 U/μL), and 2.0 μL of 10× MSP PCR buffer, and finally add ddH2O to the volume to 20 μL. The reaction conditions were 94°C for 5 min, followed by 35 cycles at 94°C for 20 s, 60°C for 30 s, and 72°C for 20 s, with a final extension step at 72°C for 5 min. The obtained PCR product was placed in a gel electrophoresis apparatus filled with 2% gel into electrophoresis separation. The obtained electrophoretic bands were purified with a commercial agarose gel DNA recovery kit (Tiangen Biotech Co., Ltd.). The cells were transfected with the purified product with the pLB vector (Tiangen Biotech Co., Ltd.). Finally, the bacterial cells were cultured on LB solid medium containing ampicillin (Beyotime Institute of Biotechnology) and then sequenced by Anhui General Biosystems, Inc. (Anhui, China).
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6

Neonatal Mouse Cochlea Culture

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The cochleae from the inner ear in neonatal (P3) mice were dissected and placed in sterile Hank’s Balanced Salt Solution under a microscope. After removing the spiral ligament, stria vascularis and spiral ganglion, the cochleae were placed in a four-well dish covered with Cell-Tak (Corning, 354,240) and cultured in DMEM-F12 medium containing B-27TM (Thermo Fisher, 17504044), N2 (Thermo Fisher, 17502001) and ampicillin (Beyotime, ST008). After incubation at 37°C in a 5% CO2 cell incubator for 12 h, the cochleae were pre-treated with 1 μM TET for 12 h and then given 0.5 mM neomycin and 1 μM TET for another 12 h.
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7

Production and Purification of HPV16 E7

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HPV16 E7 was amplified from HPV16 whole virus plasmids and cloned into the plasmid pGEX4T-2 to obtain plasmid pGEX-4 T-2-HPV16 E7. HPV16 E7 expression was induced in Escherichia coli DH5α grown in Luria-Bertani (Beyotime, China) medium supplemented with 100 mg/L ampicillin (Beyotime, China) using 0.2 mM isopropyl β-D thiogalactopyranoside (Biosharp, China), followed by incubation at 26°C for 3 h. Cells were lysed by ultrasonication (Scientzbio, China) on ice at 200 W for 3 min (5 s on and 10s off). The lysates were centrifuged and supernatants were incubated with Glutaphione Sepharose 4B beads (GE Healthcare, USA) at 4°C for 4 h to capture the GST tag-containing proteins. The GST tag was subsequently removed with Thrombin (GE Healthcare, USA; Supplementary Figure 2). Purified HPV16 E7 was used for subcutaneous immunization of female New Zealand white rabbits (3 months old, approximately 2.5 kg). Blood was collected by cardiocentesis and serum was separated for isolation of IgG antibodies with rProteinG Agarose (Invitrogen, USA). The purified polyclonal antibodies were stored in sterile glycerol (50%) at -20°C. The titer and specificity of the antibodies were verified by Western blot analysis.
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8

Recombinant Protein Purification and Refolding

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The plasmids pET-32a/edBjtshr, pET-32a/edDrtshr, pET-28a/Bjgpa2, pET-28a/Drtsha, pET-28a/Bjgpb5, and pET-28a/ Drtshb were transformed into Escherichia coli Transetta (DE3), and the cells were cultured overnight in lysogeny broth containing 100 mg/mL of ampicillin (Beyotime) (for pET-32a/ edBjtshr and pET-32a/edDrtshr) or 50 mg/mL of kanamycin (Beyotime) (for pET-28a/Bjgpa2, pET-28a/Drtsha, pET-28a/ Bjgpb5, and pET-28a/Drtshb). When OD 600 reached ;1.0, isopropyl b-D-thiogalactoside (IPTG) (Amresco, West Grove, PA) was added to the cultures at a final concentration of 1 mM, and the cultures were allowed to shake for 12 hours at 28°C. The recombinant proteins that were expressed in inclusion bodies were purified and refolded according to the method of Xu and Zhang (31) with modification of dialysis pH value. The refolded proteins were analyzed by SDS-PAGE on 12% gel and immunostained using mouse anti-His-tag antibody (32) as the primary antibody, followed by incubation with horseradish peroxidase-conjugated goat anti-mouse IgG (33) according to the method described previously by Wang et al. (34) . Protein concentrations were determined by the bicinchoninic acid methods using BSA as a standard (CWBIO, Beijing, China).
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