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Citrate

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Citrate is a salt or ester of citric acid, a compound found naturally in citrus fruits. It is commonly used in various laboratory applications as a buffer, chelating agent, and preservative. Citrate helps maintain the pH and ionic balance of solutions, and can also bind to metal ions to prevent interference in analytical procedures.

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Lab products found in correlation

Succinate, by Merck Group (7 mentions) Acetate, by Merck Group (6 mentions) Pyruvate, by Merck Group (6 mentions) Malate, by Merck Group (5 mentions) Lactate, by Merck Group (4 mentions) Oxaloacetate, by Merck Group (4 mentions) Sodium citrate, by Merck Group (4 mentions) Alanine, by Merck Group (3 mentions) Phenylalanine, by Merck Group (3 mentions) Tyrosine, by Merck Group (3 mentions) Isocitrate, by Merck Group (3 mentions) Rnaimax transfection reagent, by Thermo Fisher Scientific (3 mentions) Ammonium formate, by Merck Group (3 mentions) Streptozotocin (stz), by Merck Group (3 mentions) Formic acid, by Thermo Fisher Scientific (3 mentions) Serine, by Merck Group (2 mentions) Formate, by Merck Group (2 mentions) Isoleucine, by Merck Group (2 mentions) Histidine, by Merck Group (2 mentions) Glutamate, by Merck Group (2 mentions)

55 protocols using citrate

1

Neonatal CMs Transfection Protocol

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Neonatal CMs were transfected in vitro in the presence of Lipofectamine RNAiMAX transfection reagent (Life Technologies), used according to the manufacturer’s instructions. Cells were transfected with modRNA in vitro in sucrose citrate buffer consisting of 20 μL of a 0.3 g/mL solution of sucrose (15% sucrose) in nuclease-free water, 20 μL of 0.1 M citrate (pH 7; Sigma), and 20 μL of modRNA solution (various concentrations in saline), with the final volume made up to 60 μL with nuclease-free water (5% sucrose and 0.03 M citrate final concentration). The transfection mixture was injected directly (three individual injections, 20 μL each) into the myocardium at three different sites (two injections in the border zone and one at the heart apex).
Magadum A., Singh N., Kurian A.A., Sharkar M.T., Chepurko E, & Zangi L. (2018). Ablation of a Single N-Glycosylation Site in Human FSTL 1 Induces Cardiomyocyte Proliferation and Cardiac Regeneration. Molecular Therapy. Nucleic Acids, 13, 133-143.
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2

Synthesis and Citrate Functionalization of Mn3O4 Nanoparticles

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A template or surfactant-free sol-gel method was followed for the synthesis of bulk Mn3O4 NPs at room temperature and pressure21 (link). To functionalize the nanoparticles with ligand citrate, the as-prepared Mn3O4 NPs (~20 mg mL−1) were mixed extensively with citrate (Sigma, USA) solution (pH 7.0, 0.5 M) for 15 h in a cyclomixer. The time for mixing was carefully adjusted to have a nanomaterial in the size range of 4–6 nm. Non-functionalized larger NPs were removed using a syringe filter (0.22 μm).
Adhikari A., Mondal S., Chatterjee T., Das M., Biswas P., Ghosh R., Darbar S., Alessa H., Althakafy J.T., Sayqal A., Ahmed S.A., Das A.K., Bhattacharyya M, & Pal S.K. (2021). Redox nanomedicine ameliorates chronic kidney disease (CKD) by mitochondrial reconditioning in mice. Communications Biology, 4, 1013.
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3

Metabolite Profiling of Isotope-Labeled Compounds

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[15N1]-cholamine bromide hydrobromide salt (15N1-cholamine) was obtained from the Metabolite Standards Synthesis Center (SRI International).24 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) was purchased from ACROS organics (Thermo Fisher Scientific). The following metabolite standards and reagents were purchased from Sigma-Aldrich: isoleucine, leucine, valine, alanine, glutamate, glutamine, aspartate, glycine, phenylalanine, histidine, tyrosine, tryptophan, serine, threonine, cysteine, cystine, N-acetyl-aspartate (N-AcAsp), formate, fumarate, 3-phosphoglycerate (3-PG), citrate, malate, alpha-ketoglutarate (α-KG), succinate, pyruvate, acetate, lactate, hydrochloric acid (HCl) and sodium hydroxide (NaOH). [U-13C]-pyruvate, [U-13C]-lactate, 1-13C-acetate, 2-13C-acetate and 1,2-13C2-acetate were purchased from Cambridge Isotope Laboratories (Andover, MA). Reduced glutathione (GSH) and oxidized glutathione (GSSG) were purchased from ACROS organics (Thermo Fisher). 18 MΩ water was obtained using an ultrapure water system (Barnstead, Dubuque, IA).
Vicente-Muñoz S., Lin P., Fan T.W, & Lane A.N. (2021). NMR analysis of carboxylate isotopomers of 13C-metabolites by chemoselective derivatization with 15N-cholamine. Analytical chemistry, 93(17), 6629-6637.
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4

Antimicrobial Effects of Metabolites

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Bacteria cells were prepared as described above and resuspended in LB media, adjusted OD600 to 0.5. Colistin (2 mg/L) or/and a metabolite (1.2, 2.5, 5, and 10 mM) were added and incubated at 37°C for 6 h or 12 h. After incubation, CFU were determined by the 10-fold serial broth microdilution method. The metabolites, including pyruvic acid, citrate, α-ketoglutaric acid, cis-aconitic acid, and (s)-malate and agmatine sulfate, were all purchased from Sigma-Aldrich and dissolved in water.
Zhai Y.J., Liu P.Y., Luo X.W., Liang J., Sun Y.W., Cui X.D., He D.D., Pan Y.S., Wu H, & Hu G.Z. (2023). Analysis of Regulatory Mechanism of AcrB and CpxR on Colistin Susceptibility Based on Transcriptome and Metabolome of Salmonella Typhimurium. Microbiology Spectrum, 11(4), e00530-23.
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5

Enzyme-Mediated Biochemical Assay Protocol

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Restriction enzymes and T4 DNA ligase were purchased from New England Biolabs (Beverly, MA). Pfu DNA polymerase was from Stratagene (Agilent Technologies, Santa Clara, CA). Luria-Bertani broth mix (Becton Dickinson, Franklin Lakes, NJ) was purchased from Fisher Scientific (Suwanee, GA). Deoxyribonuclease I, citrate, MgCl2, 4-aminobenzoic acid (pABA), 5-phospho-D-ribose 1-diphosphate sodium salt (PRPP) and N-(1-naphthyl) ethylenediamine were purchased from Sigma-Aldrich Chemical Company, Inc. (St. Louis, MO). Bradford protein assay reagent and polyacrylamide gels were from Bio-Rad (Hercules, CA). Gases were obtained from Strate Welding (Gainesville, FL) and Oxygen Services (Orange, CA). All other chemicals were of reagent grade and purchased from Fisher Scientific.
Bechard M.E., Farahani P., Greene D., Pham A., Orry A, & Rasche M.E. (2019). Purification, kinetic characterization, and site-directed mutagenesis of Methanothermobacter thermautotrophicus RFAP Synthase Produced in Escherichia coli. AIMS Microbiology, 5(3), 186-204.
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6

Targeted Delivery of Luc modRNA

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Luc modRNA (25 μg) in a total volume of 60 μL in Tris-borate (TB) buffer was delivered via direct injection to the myocardium. The sucrose-citrate buffer contains 20 μL sucrose in nuclease-free water (0.3 g/mL) and 20 μL citrate (0.1 M, pH 7; Sigma) mixed with 20 μL modRNA. The transfection mixture was directly injected (three individual injections, 20 μL each) into the heart, kidney, or liver.
Sultana N., Hadas Y., Sharkar M.T., Kaur K., Magadum A., Kurian A.A., Hossain N., Alburquerque B., Ahmed S., Chepurko E, & Zangi L. (2020). Optimization of 5′ Untranslated Region of Modified mRNA for Use in Cardiac or Hepatic Ischemic Injury. Molecular Therapy. Methods & Clinical Development, 17, 622-633.
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7

HPLC-grade Solvents for STZ Prep

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HPLC-grade acetonitrile (ACN) and methanol (MeOH) were purchased from Merck (Muskegon, MI, USA). Purified water was obtained from Wahaha (Hangzhou, China). STZ and citrate were purchased from Sigma-Aldrich (St. Louis, MO, USA).
Zhang X., Liu Y., Yang S., Gao X., Wang S., Wang Z., Zhang C., Zhou Z., Chen Y., Wang Z, & Abliz Z. (2023). Comparison of Local Metabolic Changes in Diabetic Rodent Kidneys Using Mass Spectrometry Imaging. Metabolites, 13(3), 324.
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8

Cell Lysis and Fractionation Protocol

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5 × 107 CCRF-CEM cells were collected per sample and lysed in lysis buffer (25 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 5% glycerol, 1% NP-40, 10 mM β-glycerophosphate) with a protease inhibitor cocktail (Sigma-Aldrich) and other inhibitors (1 mM PMSF, 10 mM NaF, 1 mM Na3VO4). 1 mM AMP (Acros Organics) or 10 mM citrate (Sigma-Aldrich) were also added to the lysis buffer as controls where indicated. Equal amounts of protein were filtered using the Disposable Ultrafiltration Units with molecular weight 200 kD cutoff (USY-20; Advantec MFS). 30 μg of total lysate or filtrate (<200 kD) were resolved by SDS-PAGE and immunoblotted with the indicated antibodies.
Harris R., Yang M., Schmidt C., Royet C., Singh S., Natarajan A., Morris M., Frezza C, & Laman H. (2022). Fbxo7 promotes Cdk6 activity to inhibit PFKP and glycolysis in T cells. The Journal of Cell Biology, 221(7), e202203095.
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9

Investigating Cell Signaling Pathways

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The following chemical reagents were used in cell culture experiments: LPS-EB Ultrapure (1 μg/ml, Invivogen), zVAD (50 μm, SM Biochemicals), GSK 963 (100nM, GlaxoSmithKline), GSK 843 (100nM, GlaxoSmithKline), GSK 872 (100nM, GlaxoSmithKline), AP1 (100 nM, ClonTech, sold as “B/B Homodimerizer”), itaconate (1mM, Sigma), citrate (1mM, Sigma), dimethyl malonate (1mM, Sigma), 4-octyl itaconate (1mM, provided by Luke O’Neill, Trinity College, Dublin). For in vivo intracranial injections, the following concentrations were used: GSK 963 and GSK 843, 800nM; dimethyl malonate and 4-octyl itaconate, 8mM.
Daniels B.P., Kofman S.B., Smith J.R., Norris G.T., Snyder A.G., Kolb J.P., Gao X., Locasale J.W., Martinez J., Gale M J.r., Loo Y.M, & Oberst A. (2019). The nucleotide sensor ZBP1 and kinase RIPK3 induce the enzyme IRG1 to promote an antiviral metabolic state in neurons. Immunity, 50(1), 64-76.e4.
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10

Metabolite Standard Preparation for LC-MS

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LC-MS-grade acetone, acetonitrile (ACN), water, and methanol (MeOH) were purchased from Honeywell Burdick & Jackson (Muskegon, MI). Formic acid and all cell culture reagents were obtained from ThermoFisher Scientific (Waltham, MA). Citrate, succinate, α-ketoglutarate, AMP, ADP, and ATP standards were obtained from Sigma Aldrich (St. Louis, MO).
Filla L.A., Sanders K.L., Filla R.T, & Edwards J.L. (2016). Automated Sample Preparation in a Microfluidic Culture Device for Cellular Metabolomics. The Analyst, 141(12), 3858-3865.
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