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22 protocols using phosphate buffered saline (pbs)

1

Comprehensive NMR and Cell Assay Protocol

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1D-NMR experiments including 1H NMR (500 MHz) and APT 13C NMR (125 MHz) and 2D-NMR experiments including 1H−1H COSY, HSQC, HMBC, and NOESY were recorded on a Bruker Avance III HD 500 NMR instrument (Karlsruhe, Germany). Chromatographic techniques were applied to separate compounds, including open columns chromatography using silica gel 60 (0.063 - 0.200 mm), flash column chromatography (FCC) using silica gel 60 (0.040 - 0.063 mm), and thin layer chromatography (TLC) using pre-coated silica gel 60 F254 plates (Merck, Darmstadt, Germany). The solvents were obtained from Merck (Darmstadt, Germany). A human breast adenocarcinoma (MCF-7) cell line was obtained from the Iranian Biological Resource Center, Tehran, Iran. RPMI 1640, phosphate-buffered saline (PBS), and fetal bovine serum (FBS) were acquired from Biosera (Ringmer, UK). Penicillin/streptomycin and cisplatin were obtained from EBEWE Pharma (Unterach, Austria). Also, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was taken from Sigma-Aldrich (St. Louis, MO, USA). Hydrochloric acid 32% and chloramphenicol were acquired from Sigma-Aldrich. Finally, p-iodonitrotetrazolium violet (INT) was obtained from Fluka (Germany).
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2

Xenograft Tumor Model in Nude Mice

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Twenty-five healthy male athymic BALB/c (nu/nu) nude mice were purchased from the SLAC Laboratory Animal Co., Ltd. (Shanghai, China). The mice were 6 weeks old and weighed 18–20 g. The mice were housed and fed in a specific pathogen-free (SPF) environment and provided with sterile food and water. All procedures were performed under aseptic condition. Before the animal experiments, the mice were fed ad libitum for one week in the new environment.
Cultured cells were washed with phosphate-buffered saline (PBS) (Biosera, Boussens, France), and 0.2 mL of cell suspension (1×107 cells) was injected into the skin of the right underarm region of five nude mice.
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3

Reagents and Materials for Biological Assays

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Brain heart infusion (BHI) broth, malt extract agar, and Ringer’s solution were obtained from LABM (Heywood, UK). Ciproxin was obtained from Oxoid Ltd. (Basingstoke, UK) and amphotericin B from Mast Group Ltd. (Merseyside, UK). Dulbecco’s Modified Eagle’s Medium (DMEM), DMEM high glucose, RPMI media, and low melting agarose were purchased from Gibco® (Gaithersburg, MD, USA). Fetal bovine serum (FBS), trypsin, penicillin/streptomycin, trypan blue 0.5%, and phosphate-buffered saline (PBS) were purchased from Biosera (Boussens, France). Dimethyl sulfoxide (DMSO) and propidium iodide were purchased from Biotium (Hayward, CA, USA), while hydrogen peroxide, ABTS, potassium persulfate, ascorbic acid, sulforhodamine B (SRB), Trizma base, and etoposide were purchased from Sigma-Aldrich (St. Louis, MO, USA). TrichloroAcetic acid (TCA) was obtained from MP Biomedicals (Santa Ana, CA, USA). Acetic acid and ethanol were purchased from Scharlau (Barcelona, Spain) and DPPH from Calbiochem® (Darmstadt, Germany).
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4

Cytotoxicity Assay with Cell Culture Reagents

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Dulbecco’s Modified Eagle’s Medium (DMEM), DMEM high glucose, and RPMI media were purchased from Gibco® (Gaithersburg, MD, USA). Fetal bovine serum (FBS), trypsin, penicillin/streptomycin, and phosphate buffered saline (PBS) were purchased from Biosera (Boussens, France). DMSO, acetic acid, TCA, Trizma base, and sulforhodamine B (SRB) were purchased from Sigma-Aldrich (Steinheim, Germany). Annexin V-PI kit was purchased from BD Biosciences (San Jose, CA, USA).
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5

Biosurfactant Extraction and Purification

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The biosurfactants were provided by our project partners from Ulster University as part of the MARISURF EU Horizon 2020 project. The extraction and purification methods were described in detail previously [11 (link),12 (link)]. The human cell lines were obtained from the American Type Culture Collection (ATCC, Rockville, MD, USA). Dulbecco’s Modified Eagle’s Medium (DMEM, high glucose), penicillin/streptomycin, fetal bovine serum, and phosphate-buffered saline were obtained from Biosera (Boussens, France). BEGM medium was from Lonza (Lonza/Clonetics Corporation, Walkersville, MD, USA) DPPH, ABTS, and low melting point agarose were purchased from Sigma-Aldrich (BioUltra, Darmstadt, Germany). Resazurin sodium salt and propidium iodide were purchased from Sigma-Aldrich (St. Louis, MO, USA). Crodasinic LS30 and Texapon N70 were supplied by DeWolf Chemical (Warwick, RI, USA).
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6

Cell Culture and Analytical Methods

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Dulbecco’s modified Eagle’s medium (DMEM; high glucose), fetal bovine serum (FBS), trypsin, penicillin-streptomycin, and phosphate-buffered saline (PBS) were purchased from Biosera (Boussens, France). Dimethyl sulfoxide (DMSO), acetic acid, trichloroacetic acid (TCA), Trizma base, sulforhodamine B (SRB), agarose, DPPH, ABTS, and ascorbic acid were purchased from Sigma-Aldrich (BioUltra, Darmstadt, Germany). The pUC19 plasmid DNA was a gift from Joachim Messing (Addgene plasmid # 50005). NucleoZOL was purchased from Macherey-Nagel (Düren, Germany), whereas all primers, dNTPs, random hexamers, and PrimeScript reverse transcriptase were from Invitrogen (ThermoFisher Scientific, Waltham, MA, USA). The KAPA SYBR Fast Master Mix solution was obtained from Kapa Biosystems (Hoffmann-La Roche, Basel, Switzerland).
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7

Cytotoxicity Evaluation of Cell Lines

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Dulbecco’s Modified Eagle’s Medium (DMEM) and Fungizone (Amphotericin B) were purchased from Gibco (Waltham, MA, USA). Fetal bovine serum (FBS), trypsin, penicillin/streptomycin, and phosphate-buffered saline (PBS) were purchased from Biosera (Boussens, France). MRS Broth, LAB094 was purchased from LabM (Bury, UK). The Annexin V/PI kit was purchased from BD Biosciences (Franklin Lakes, NJ, USA). Acetic acid, trichloroAcetic acid (TCA), Trizma base, sulforhodamine B (SRB), NaHSeO3 and all other chemicals mentioned were purchased from Sigma-Aldrich (St. Louis, MO, USA).
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8

Soil Bacteria Extraction Protocol

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Soil samples (10 g) were weighed and placed into a 50 mL centrifuge tube to which 20 mL of phosphate buffered saline (PBS) (Biosera, France) was added. The tubes were then shaken at room temperature for 30 minutes at 150 rpm in New Brunswick Benchtop Incubator Shaker Innova 40/40R (Eppendorf, Germany). The supernatant was then transferred to a new 50 ml tube, and the washing step was repeated. This was followed by transferring the supernatant into a 50 mL tube with centrifugation at 200 × g for 1 minute. The supernatant was transferred into a new 50 ml tube and centrifuged at 12,600 × g for 25 minutes. The pellet was suspended in 3 ml of sterile PBS and stored at -20°C.
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9

Cell Apoptosis and Oxidative Stress Assays

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Dulbecco's Modified Eagle's Medium (DMEM) and Fungizone (Amphotericin B) were purchased from Gibco (Gaithersburg, MD, USA). Fetal bovine serum (FBS), trypsin, penicillin/streptomycin, and phosphate-buffered saline (PBS) were purchased from Biosera (Boussens, France). MRS Broth, LAB094 and Agar No. 2 (MC006) were purchased from LabM (UK). The Annexin V-PI kit was purchased from BD Biosciences (USA). The Human Apoptosis Antibody Array kit (ARY 009) from R&D systems (USA) was used. Carboxy-H2DCFDA (C400) was purchased from Invitrogen (Invitrogen, USA). Acetic acid, trichloroAcetic acid (TCA), Trizma base, NaHSeO3, H2O2 and sulforhodamine B (SRB) were purchased from Sigma-Aldrich (Germany).
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10

Bee Homogenization and Viral Nucleic Acid Extraction

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For each sample, six bees were homogenized with garnet beads (PowerBead Tubes, 0.7 mm, MO BIO Laboratories, USA) in phosphate-buffered saline (Biosera, France) by vortexing (3500 rpm/2 min).
Homogenates were centrifuged for 1 min at 13,000 rpm and next viral DNA and RNA were extracted from 100 µl of the supernatants using TRI Reagent (Sigma Aldrich, USA) according to manufacturer's instructions. Obtained nucleic acids were stored at -80 °C until further use.
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