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10 protocols using phosphate buffered saline (pbs)

1

Culturing Rat Pheochromocytoma PC-12 Cells

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The PC-12 pheochromocytoma cell line derived from rat adrenal medulla was obtained from American Type Culture Collection (Manassas, VA). RPMI-1640, trypsin solution, phosphate-buffered saline, fetal bovine serum (FBS), sodium pyruvate (0.1 M), L-glutamine (0.2 M) and penicillin/streptomycin solution (containing 10,000 units·ml−1 penicillin and 10,000 μg·ml−1 streptomycin) were obtained from Quality Biological (Gaithersburg, MD), horse serum (heat inactivated) was purchased from Biosource (Rockville, MD) and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) buffer [1 M, pH 7.4] was obtained from Mediatech, Inc. (Manassas, VA). The PC-12 cells were maintained in RPMI-1640 supplemented with 1 mM HEPES buffer, 10% horse serum, 5% FBS, 1% sodium pyruvate, 1% L-glutamine and 1% penicillin/streptomycin.
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2

Murine Lung Decellularization Protocol

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The murine lungs were decellularized using a modification of a previously described 25 hour treatment protocol (Jensen et al., 2012 ). Briefly, heart-lung blocks were harvested with bicaval and aortic transection followed by tracheal and pulmonary artery cannulation. After serial 3cc flushes of 5% Penicillin-Streptomycin (Life Technologies, Carlsbad, CA, USA), 0.1% Triton-X-100 (Sigma-Aldrich, St. Louis, MO, USA) was instilled in the trachea followed by an 8 hour incubation at 27°C. The lungs were rinsed and a 2% sodium deoxycholate (Sigma-Aldrich, St. Louis, MO, USA) (w/v) solution was instilled into the trachea and pulmonary circulation. The lungs were incubated for an additional 14 hours at 4°C, followed by a 1 hour flush with a 1M NaCl solution (27°C). Finally, the lungs were treated with a 30ug/mL bovine pancreatic DNAse (Sigma-Aldrich, St. Louis, MO, USA) solution for 1 hour at 27°C. Specimens were stored in phosphate buffered saline (Quality Biological, Gaithersburg, MD, USA) with 5% Penicillin-Streptomycin (Life Technologies, Carlsbad, CA, USA) at 4°C until further use.
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3

Decellularization of Murine Lungs

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The murine lungs were decellularized using a modification of a previously described 24 hr treatment protocol (Jensen et al., 2012 ). Briefly, the lungs were flushed in situ with distilled water (dH2O) The cardiopulmonary organs were harvested en bloc and submerged in dH2O for 1 h at 4°C. The lungs were exposed to 3 sequential treatments: (1) a flush with 0.1% Triton X-100 (SigmaAldrich) in dH2O and incubation for 24 h at 4°C; (2) a flush with 2% sodium deoxycholate (Sigma-Aldrich) in dH2O and incubated for 24 h at 4°C; and (3) a flush with 1 M sodium chloride solution and incubation for 1 h at room temperature. Finally, the lungs were treated with a 30 ug/mL bovine pancreatic DNAse (Sigma-Aldrich) solution for 1 hr at 27°C. Specimens were stored in phosphate buffered saline (Quality Biological, Gaithersburg, MD) with 5% Penicillin-Streptomycin (Life Technologies, Carlsbad, CA) at 4°C until further use.
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4

Optical Fiber-Based Heparin Sensing

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Nile blue A and polyethylene glycol (Mn 7,000–9,000) (Bioultra 8000) were purchased from Sigma Aldrich Inc. and used as received. Phosphate buffered saline was purchased from Quality Biological and used without further purification. Methanol was purchased from Fisher and used without further purification. Whatman No. 2 filter paper circles were purchased from GE Healthcare, U.K. A multi-mode optical fiber with core diameter of 400 μm were purchased from Thorlabs, USA. Miniature Heat-Shrink Tubing was purchased from McMaster-Carr, USA. Transpore tapes were purchased from 3M. Unfractionated heparin (1000 U/ml) was purchased from McKesson Corporation, USA. Polytetrafluoroethylene (PTFE) tubing was purchased from Agilent Technologies.
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5

Stability of Nucleic Acid Samples

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N1 and N2 were each diluted either in PBS (Quality Biological, Gaithersburg, MD) or DPBS (Thermo Fisher Scientific, Waltham, MA). The recipe for PBS, as provided by the manufacturer, is sodium phosphate dibasic (795 mg/l, 5.6 mM), potassium phosphate monobasic (1.06 mM), and sodium chloride (9000 mg/l, 154 mM). The recipe for DPBS, as provided by the manufacturer, is calcium chloride (100 mg/l, 0.9 mM), magnesium chloride (100 mg/l, 0.49 mM), potassium chloride (200 mg/l, 2.66 mM), potassium phosphate monobasic (200 mg/l, 1.47 mM), sodium chloride (8000 mg/l, 137.93 mM), and sodium phosphate dibasic (2160 mg/l, 8.06 mM). Samples were stored at −80 °C and at 4 °C for a total of eight different sets of combinations of buffer and temperature conditions. NA stored at −80 °C was thawed at each timepoint and then returned to frozen storage until the next timepoint. NA activity was tested at weeks 0, 4, 12, 24, and 36. NA in PBS at week 36 was subsequently “rescued” through dilution in DPBS to compare its activity to NA in PBS at 36 weeks and NA in DPBS at 36 weeks. The stability experiment was also repeated with N1 in PBS, N1 in DPBS, N2 in PBS, and N2 in DPBS at RT and activity was tested at weeks 0, 3, 8, 12, and 24.
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6

Modulating Viral Infection Dynamics

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Viral infection was performed as previously described with some modifications. An MOI of 0.1 for 5 h (low) or 30 for 4 h (high) was used for all infections. Virus particles were diluted in serum-free media, added to the cells, and incubated at 37°C for 1 h. The cells were washed with PBS (Quality Biological, 114–058-101) twice and overlaid with basal media until the end of the infection. For starvation before infection, cells were washed in PBS then starved for 4 h with starvation media [25 (link)]. This amino acid-deficient media is used to induce autophagic flux: 140 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, 5 mM glucose, 20 mM HEPES, pH 7.4, and 1% BSA (Fisher bioreagents, CAS 9048–46-8). Starvation media was added before infection, after which they were infected as the infection-only group. For starvation after infection, the cells were infected for 1 h (adsorption) and washed twice with PBS before being overlaid with starvation media for 4 h. The cells were either fixed and prepared for immunofluorescence assay or electron microscopy or collected in microcentrifuge tubes and stored at −80°C for plaque assay-based viral titer determination.
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7

KCNQ1/KCNE1 Channel Dynamics

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HEK293T cells (ATCC: The Global Bioresource Center) were cultured in 35-mm petri dishes in DMEM (Corning Cellgro, 15-013-CV) supplemented with 10% FBS (Sigma-Aldrich) and 1%GlutaMax (Cellutron Life Technologies) under 5% CO2 at 37 °C. Cells were transiently transfected with the plasmid DNA of interest using FuGene HD following manufacturer’s instruction (Promega). Equal amount of plasmid DNA of KCNQ1 (or KCNQ1-GFP or its mutants) and KCNE1 were used. Confocal images and current recordings were conducted 48–56 h after transient expression of the channels.
HEK293T cells were transfected with GFP-tagged KCNQ1 (1.5 µg) and KCNE1(1.5 µg). 6 h after transfection, cells were plated on glass bottom dishes (MatTek Corporation). Forty-eight hours after transfection, cells were washed two times with PBS (Quality Biological) and incubated at 37 °C for treatment in extracellular recording solution (below). For all treatments, cells were incubated at 37 °C, 5% CO2. DMSO treated cells were used as control for PAO (2 μM) and WMN (0.01 μM, 5 μM) treatment. Rapamycin (1 μM) was applied for 30 min to induce PJ, PJ-SAC, PJ-INPP5E, or PJ-DEAD translocation to the plasma membrane. Confocal images and patch clamp experiments were performed at room temperature immediately after treatment.
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8

SARS-CoV-2 Lung Viral Titer Quantification

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SARS-CoV-2 lung titers were quantified by homogenizing harvested lungs in PBS (Quality Biological Inc.) using 1.0 mm glass beads (Sigma Aldrich) and a Beadruptor (Omini International Inc.). Homogenates were added to near-confluent Vero E6 cultures and SARS-CoV-2 virus titers determined by counting plaque forming units using a 6-point dilution curve.
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9

Visualization of Insect Chemosensory Tissues

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Live antennal, palp and labella tissues were dissected in 0.1M PBS (119-069-131, Quality Biological) and immediately mounted in Slow-Fade Gold Antifade Mountant (Invitrogen, S36936) on glass slides. Images were acquired on a Zeiss LSM 880 Airyscan Fast confocal microscope within 2 h of dissection. The 488 nm laser line was used to excite the green GCaMP6f signal. An additional DIC channel was used to visualize bright field morphology of the peripheral tissue. Images of the antennae, palps, and labella were acquired with a 40X oil immersion objective. Images were processed using Fiji.75 (link) A maximum intensity projection was acquired for all z-slices of the GCaMP6f images.
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10

Quantifying SARS-CoV-2 Lung Titers

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SARS-CoV-2 lung titers were quantified by homogenizing harvested lungs in PBS (Quality Biological Inc.) using 1.0 mm glass beads (Sigma-Aldrich) and a Beadruptor (Omni International Inc.). Homogenates were added to Vero E6 cells. SARS-CoV-2 virus titers determined by counting plaque-forming units (PFU) using a 6-point dilution curve.
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