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Sodium bicarbonate

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Sodium bicarbonate is a white, crystalline powder that is commonly used in various laboratory applications. It is a chemical compound with the formula NaHCO3. Sodium bicarbonate is a versatile and widely-used substance in the field of chemistry and biochemistry.

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1 275 protocols using sodium bicarbonate

1

Cell Line Cultivation and Maintenance

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The NIH-3T3, Hs68, RBL-2H3, and RAW264.7 cell lines were purchased from the Bioresource Collection and Research Center (BCRC, Hsinchu City, Taiwan).
As a mouse fibroblast cell line, NIH-3T3 was cultured with Dulbecco's modified Eagle's medium (DMEM, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 10% calf serum (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1.5 g/L sodium bicarbonate (Sigma-Aldrich, St. Louis, MO, USA), 4 mM L-glutamine (Sigma-Aldrich, St. Louis, MO, USA), and 4.5 g/L glucose (Sigma-Aldrich, St. Louis, MO, USA).
As a human fibroblast cell line, Hs68 was cultured using DMEM containing 4 mM L-glutamine, 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, and 10% FBS (Gibco, Thermo Fisher Scientific, Waltham, MA, USA).
The rat basophilic leukemia (RBL)-2H3 cell line was cultured using Eagle's minimum essential medium (EMEM, Sigma-Aldrich, St. Louis, MO, USA) supplemented with 4 mM L-glutamine, 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, 1.0 mM sodium pyruvate, and 15% FBS.
As a murine macrophage cell line, RAW264.7 was cultured with DMEM containing 4 mM L-glutamine, 1.5 g/L sodium bicarbonate, and 10% FBS.
All cell lines were consistently maintained and kept within a humid chamber set to 37°C with 5% CO 2 , which were struck twice per week using standard procedures.
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2

Cytotoxic Effects of MTX and DOX

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In this experimental study, 50 mg/ml MTX and 2 mg/ml DOX were purchased from Helale ahmar pharmacy (Iran). MTX was also purchased from Sigma (Sigma, USA) and dissolved in 0.5% sodium bicarbonate (Merk, Germany).
PLC/PRF/5, a hepatocellular cell line, was purchased with NIH-3T3 cell line and human primary neuroblastoma cells from Pasteur Institute of Iran. The cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 35 µg U/ml penicillin (Sigma, USA), 50 µg/ml streptomycin (Sigma, USA) and 2 mg/ml sodium bicarbonate (Merk, Germany), and kept in a humidified atmosphere with 5% CO2 at 37˚C. The cell-harvesting process was performed by 0.25% trypsin solution (Sigma, USA) with 0.03% Ethylene di-amine tetra-acetic acid (EDTA, Sigma, USA).
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3

Comprehensive Reagent Sourcing Protocol

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McCoy’s 5A medium, sodium bicarbonate, and dimethyl sulfoxide (DMSO) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Paclitaxel, one of the most effective and widely used anti-cancer drugs for treating various tumors, was purchased from LC Laboratories (MO, USA). Bovine serum albumin (BSA), sodium bicarbonate, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and other chemicals such as rhodamine-123, propidium iodide (PI), RNase A, sodium citrate, and standards for analysis were obtained from Sigma-Aldrich (St. Louis, MO, USA). All other chemicals and reagents for cell culture (DMEM/F12 medium, fetal bovine serum (FBS), epidermal growth factor, fibroblast growth factor, insulin, penicillin, and streptomycin) were purchased from Gibco (Grand Island, NY, USA). Coomassie Brilliant Blue R-250 was purchased from Bio-Rad (Hercules, CA, USA). Analytical-grade solvents used during the purification procedures, including acetonitrile, n-butanol (Bu), ethanol, ethyl acetate (EtOAc), hexane, and methanol were obtained from Merck (Darmstadt, Germany).
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4

Fabrication of Porous PVA Scaffolds

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Polymer scaffolds were manufactured by utilizing an FDA approved biodegradable PVA. In particular, a PVA solution was prepared by dissolving 8 g PVA powder (Sigma Aldrich, 99% hydrolyzed, MW = 89 000–98 000) in 40 ml deionized water, and stirred at 80 °C until the PVA reached a final concentration of 21% w/v. After cooling it to room temperature (RT), 3 g of the obtained PVA solution was stirred with 0.66 g of sodium bicarbonate (Sigma Aldrich).
The mixture composed of PVA and sodium bicarbonate was mixed for 30 seconds with 1 ml hydrochloric acid (HCl) (37% purity, Carlo Erba). The chemical reaction of hydrochloric acid with sodium bicarbonate particles generates carbon dioxide gas that, due to the high viscosity of the polymer, remains trapped inside of the polymer, and induces the formation of the PVA foam (Fig. 1a).27 (link) The produced PVA foam was cast in a polystyrene mold (2 cm diameter) (Fig. 1b). The mold was quickly frozen at −20 °C for 6 h, to have the PVA foam stabilized (Christ alpha 1-4 lsc). The samples were freeze-dried at −20 °C under a vacuum pressure of 0.250 mbar for 24 h (Fig. 1c).28 (link) The scaffold was extracted from the mold (Fig. 1d), and washed in deionized water to remove traces of unreacted components. The samples were placed to dry under a hood, and, once dried, the non-porous external surfaces of the scaffolds were cut with a surgical scalpel.
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5

Iridium Catalyst Synthesis and Photocatalytic System

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For catalyst synthesis, the following chemicals were obtained from commercial sources and used without further purification unless otherwise specified: 2-(pyridine-2-yl)propan-2-ol (95%, Strem Chemicals), dichloro-(pentamethylcyclopentadienyl)-iridium(iii) dimer ([Cp*IrCl2]2, 98%, Strem Chemicals), sodium bicarbonate (99.7%, Sigma), acetone (99.9%, Sigma), magnesium sulfate anhydrous (95%, Fisher), NaIO4 (99.8%, Sigma), ITO (99.5%, light green, 17–28 nm particle size, 30–50 m2 g−1, Alfa Aesar) and CeO2 (light yellow, <25 nm particle size, 55 m2 g−1, Sigma).
For the photocatalytic system, the following chemicals were used: sodium sulfate decahydrate (>99%, Acros Organics), sodium bicarbonate (>99.7%, powder, Sigma-Aldrich), tris(2,2′-bipyridyl)ruthenium(ii) chloride hexahydrate (>98%, Strem Chemicals), sodium hexafluorosilicate (powder, Aldrich Chemistry), sodium persulfate (>99.7%, Honeywell).
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6

Adipogenesis Regulation by B. pilosa Extract

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Dexamethasone (Dex), insulin, isobutylmethylxanthine (IBMX), Oil Red O powder, rosiglitazone (RGS), sodium bicarbonate, methylthiazoletetrazolium (MTT), Tween 20, isopropanol, formaldehyde, glutamine, glucose, sodium pyruvate, sodium bicarbonate, pantothenic acid, cortisol, triiodothyronine, methanol, and butanol were purchased from Sigma-Aldrich (St. Louis, MO, USA). Penicillin/streptomycin solution, Dulbecco’s Modified Eagle’s Medium (DMEM) and fetal bovine serum (FBS) were obtained from Hyclone Laboratories, Inc. (Logan, UT, USA) and Life Technologies Corp. (Grand Island, NY, USA). B. pilosa extract and GHT were produced in compliance to the good manufacturing practices guidelines and purchased from Chun-Yueh Biomedical Technology Co. (Taipei, Taiwan) as previously described22 (link). Quality control of GHT in each batch of B. pilosa extracts was conducted as shown in Sup. Fig. S3 as previously described22 (link).
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7

Cytotoxicity Assay of Bioactive Compound

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Dulbecco's Modified Eagle's Medium (DMEM), RPMI-1640, ethylenediaminetetraacetic acid, gentamicin sulfate, streptomycin sulfate, penicillin G, trypsin, sodium bicarbonate, phosphate buffered saline, cholera toxin, insulin, sulforhodamine B (SRB), trichloroacetic acid (TCA), hydrocortisone, epidermal growth factor (EGF), sodium bicarbonate, and GN were procured from Sigma Chemical Co., (St. Louis, MO, USA). Horse serum and fetal bovine serum (FBS) were from GIBCO (Life Technologies). CC was obtained from CSIR – Central Drug Research Institute (CDRI), Lucknow, Uttar Pradesh, India.
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8

Cultivation and Infection of Cell Lines

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Three batches of RM, IR-P1 (Merial, France) and BHK-21 were cultured in 48 well plates (Nunc MicroWell Thermo Fisher). RM cells were cultured in RM media; Minimum Essential Medium ((MEM), Thermo Fisher) 5% new born calf serum (Gibco), 20U/mL penicillin (Gibco), 2.5% lactalbumin hydrolysate (Gibco) and sodium bicarbonate (Sigma Aldrich) at pH 7.4 to 7.6) and a seeding density of 1.5x105 cells/mL. IR-P1 cells were propagated in IR-P1 media; MEM (Thermo Fischer), 10% new born calf serum (Gibco), 20U/mL penicillin (Gibco), 2.5% lactalbumin hydrolysate; (Gibco) and sodium bicarbonate (Sigma Aldrich) at pH 7.4 to 7.6) and a seeding density of 2x105 cells/mL. BHK-21 cells were propagated in complete growth medium for BHK cells; alpha MEM (Thermo Fisher) 2 mM-glutamine (Gibco), 20U/mL penicillin (Gibco) and 5% fetal bovine serum (Gibco), at pH 7.2 to 7.4 and a seeding density of 7.5x 105 cells/mL.
Each well of the 48 well plates was inoculated with 200 μL of the cell suspension. The plates were then incubated at 37 °C in a 5% CO2 incubator (Thermo Scientific. Jouan). The plates were monitored daily under the microscope for confluence (Olympus, Model: CKX 31). Cells were infected at 90–100% confluence.
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9

Culturing Synchronized P. falciparum Parasites

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P. falciparum parasites were cultured in human erythrocytes50 (link) and were synchronised by sorbitol treatment51 (link). NF54-based lines were cultured at 2% haematocrit in human O + erythrocytes (purchased from pooled, anonymous donors at the New York Blood Center) in RPMI 1640 medium (KD Medical) supplemented with 0.21% sodium bicarbonate (Sigma Aldrich), 10 μg/mL gentamicin (Fisher) and 10% O + human serum. Dd2-B2-PfATP4G358S and Dd2-B2 parasites were cultured at 3% haematocrit in human O + erythrocytes in RPMI-1640 media, supplemented with 25 mM HEPES (Fisher), 50 mg/L hypoxanthine (Sigma Aldrich), 2 mM l-glutamine (Cambridge Isotope Laboratories, Inc.), 0.21% sodium bicarbonate (Sigma Aldrich), 0.5% (wt/vol) AlbuMAXII (Invitrogen), 7.5% O + human serum and 10 μg/mL gentamicin (Fisher). Cultures were maintained at 37 °C in an atmosphere consisting of 5% O2, 5% CO2 and 90% N2.
For all other parasites, the cultures, which typically had a haematocrit between 2-4%, were maintained with continuous shaking52 (link) at 37 °C in a low-O2 atmosphere (1% O2, 3% CO2 and 96% N2). The culture medium was RPMI 1640 containing 25 mM HEPES (Gibco) supplemented with 11 mM additional glucose, 0.2 mM hypoxanthine, 20 μg/mL gentamicin sulphate and 3 g/L Albumax II. The blood was provided by Australian Red Cross Lifeblood without disclosing the identities of the donors.
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10

Ferrioxalate-Catalyzed Degradation of 124-TCB

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124-TCB (Sigma-Aldrich, Darmstadt, Germany, ≥99%) was used as the target pollutant. The ferrioxalate solution, the catalyst of the process, was prepared using potassium oxalate monohydrate (Sigma-Aldrich, 99.50%) and iron (III) sulphate hydrate (Sigma-Aldrich, 97%). Hydrogen peroxide (35 wt.%), titanium oxysulfate (used for the quantification of Hydrogen peroxide), sodium carbonate, sodium bicarbonate, sulfuric acid, oxalic acid, acetone (used for Ionic Chromatography analysis), 1,10-phenanthroline, sodium acetate (used in the measurement of iron in solution), n-hexane, tetrachloroethane, butyl cyclohexyl (used in COC determination by GC), NaOH (for pH adjustment), catalase, sodium bicarbonate, and sodium chloride were all purchased from Sigma-Aldrich. The bacteria Vibrio fischeri (Microtox® Acute Reagent, Azur Environmental, Carlsbad, CA, USA) was supplied by I.O. Analytical. All the stock solutions and their dilutions were prepared with high-purity water from a Millipore Direct-Q system (Millipore Corporation, Burlington, MA, USA) (resistivity >18 MΩ cm at 25 °C).
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