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Amicon ultra 0.5 centrifugal filter

Manufactured by Merck Group
Sourced in United States, Ireland, Germany, France

The Amicon Ultra-0.5 centrifugal filter is a lab equipment product designed for sample preparation and concentration. It utilizes centrifugal force to separate and concentrate molecules or particles from a liquid sample based on their size and molecular weight.

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75 protocols using amicon ultra 0.5 centrifugal filter

1

Gel Electrophoresis and DNA Purification

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Magnesium chloride, TRIS acetate EDTA (TAE) buffer, TRIS-base, sodium chloride, Phosphate Buffer Saline, ethidium Bromide solution (10 mg/mL), Pluronic F-127 (#540025–50ML) and Amicon ultra 0.5 centrifugal filter (#UFC5003) were provided by Sigma-Aldrich. Nuclease free water was purchased from Integrated DNA Technologies, Inc. (IDT). The DNTPs mix (#N0447S), the DNA ladder (Quick-Load® Purple 2-Log DNA ladder 0.1–10 kb, #N0550S) were provided by New England Biolabs (NEB), The polymerase enzyme (Accustart Taq DNA polymerase HiFi, #95085–05K) was provided by Quanta Biosciences. Low melt agarose was purchased from IBI Scientific (#IB70058) and the agarose from Seakem, Inc. G-capsule for electroelution (#786–001) was purchased from G-Biosciences and Freeze ‘N Squeeze DNA gel extraction columns by Bio-rad, Inc. (#732–6165). The Zymoclean Gel DNA recovery kit (#D4008) was purchased from Zymo Research, Inc. The SybrSafe DNA staining reagent was provided by Thermo Fisher Scientific, Inc. PEG3500 (#A4010–1/MAL-PEG3500-MAL) and PEG2000 (#A4010–1/MAL-PEG2000-MAL) bismaleimide were purchased from JenKem Technology.
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2

SEC Sample Preparation for Proteomics

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SEC samples were prepared as described in (Bludau et al. 2020 (link)). HEK293XT cells (20–30 million per replicate, n=3) were harvested at ~80% confluence by scraping in ice cold 1X PBS with 5nM EDTA, washing and pelleting, before being flash frozen in liquid nitrogen and stored in −80°C. Pellets were lysed in ice cold lysis buffer (150 mM NaCl, 50 mM Tris pH 7.5, 1% IGPAL-CA-630, 5% Glycerol, same lysis conditions as for IP) supplemented with 50 mM NaF, 2 mM Na3VO4, 1 mM PMSF, and 1X protease inhibitor cocktail (Sigma) and incubated on ice for 30 minutes. Cell lysates were then clarified by centrifugation for 10 minutes at 10,000 g and 4°C, followed by ultracentrifugation for 20 minutes at 100,000 g and 4°C. Samples then underwent buffer exchange into SEC buffer (50 mM HEPES pH 7.5, 150 mM NaCl and 50 mM NaF) to dilute lysis detergents on a 30 kDa Amicon ultra-0.5 centrifugal filter (Sigma). Buffer exchange was done in iterative steps of no larger than 1:3 dilutions to reach a final dilution ratio of 1:50 (IP lysis buffer: SEC buffer). The lysate underwent a final clarification by 5 minutes of centrifugation at 17,000 g and 4°C. The supernatant concentration was measured by Nanodrop spectrophotometer (Thermo Scientific) and adjusted to 20 mg/mL.
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3

Gel Electrophoresis and DNA Purification

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Magnesium chloride, TRIS acetate EDTA (TAE) buffer, TRIS-base, sodium chloride, Phosphate Buffer Saline, ethidium Bromide solution (10 mg/mL), Pluronic F-127 (#540025–50ML) and Amicon ultra 0.5 centrifugal filter (#UFC5003) were provided by Sigma-Aldrich. Nuclease free water was purchased from Integrated DNA Technologies, Inc. (IDT). The DNTPs mix (#N0447S), the DNA ladder (Quick-Load® Purple 2-Log DNA ladder 0.1–10 kb, #N0550S) were provided by New England Biolabs (NEB), The polymerase enzyme (Accustart Taq DNA polymerase HiFi, #95085–05K) was provided by Quanta Biosciences. Low melt agarose was purchased from IBI Scientific (#IB70058) and the agarose from Seakem, Inc. G-capsule for electroelution (#786–001) was purchased from G-Biosciences and Freeze ‘N Squeeze DNA gel extraction columns by Bio-rad, Inc. (#732–6165). The Zymoclean Gel DNA recovery kit (#D4008) was purchased from Zymo Research, Inc. The SybrSafe DNA staining reagent was provided by Thermo Fisher Scientific, Inc. PEG3500 (#A4010–1/MAL-PEG3500-MAL) and PEG2000 (#A4010–1/MAL-PEG2000-MAL) bismaleimide were purchased from JenKem Technology.
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4

Formulation of Thermoresponsive Hydrogel

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The alginate, P407, and pNIPAAM solutions were prepared by dissolving each polymer in a citrate–phosphate solution with the last two in an ice bath. Polymer was gradually added under magnetic stirring until apparent solution homogeneity was achieved. The final solutions were kept at 4 °C for 48 h under slight magnetic stirring until the polymer fully dissolved. The concentrations of the pNIPAAM and P407 solutions were 10 and 250 mg/mL, respectively. The sodium alginate was dissolved in a citrate–phosphate solution at 40 °C. Alginate was added to the citrate–phosphate solution under gentle magnetic stirring. The resulting 10 mg/mL solutions were then magnetically stirred at room temperature overnight. Finally, the pNIPAAM, alginate and P407 solutions were kept at 4 °C for 24 h. The sdAb solutions were concentrated up to 6.5 mg/mL using the Amicon® Ultra-0.5 centrifugal filter from Sigma-Aldrich (Saint-Quentin-Fallavier, France). The sdAb and polymer solutions were mixed at a ratio of 1:4 (v/v). The resulting concentrations of sdAb, pNIPAAM, alginate, and P407 were 1.5, 8, 8, and 200 mg/mL, respectively. To improve the solutions’ homogeneity, they were mixed by means of multiple pipetting, left at 4 °C for 24 h, pipetted a second time, and then stored at 4 °C.
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5

Purification of Flag-tagged Proteins from HEK293T Cells

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For protein purification from HEK293T cells, Flag-tagged G6PD, G6PDm1, G6PDm2, NADK1, and Flag-NADK1∆N in the pRK5 plasmid were transfected via Lipofectamin 2000. 48 hr later, cells were harvested using IP lysis buffer (20 mM Tris-HCl at pH 7.4, 150 mM NaCl, 0.5% Triton X-100, 0.5% NP-40, and 10% glycerol). Lysates were sonicated for 10 seconds and centrifuged at 17,000 x g at 4 °C for 15 min. Supernatants were incubated with anti-Flag M2 Affinity Gel at 4 °C overnight. Gel was sequentially washed with lysis buffers containing 50, 200, 400, 200, and 50 mM KCl, respectively (once each), and then with Tris buffer (100 mM Tris-HCl with 10% glycerol, pH 8.0). Recombinant proteins were eluted using 0.2 mg/ml 3xFlag peptide at 4 °C for 1 hr and concentrated by Amicon Ultra-0.5 Centrifugal Filter (Sigma-Aldrich). Protein concentration was determined by SDS-PAGE and Coomassie Blue staining, along with a protein standard (BSA).
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6

Single-Domain Antibody Purification and Characterization

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The sdAbs were concentrated to 3 mg/mL using the Amicon® Ultra-0.5 centrifugal filter from Sigma-Aldrich (Saint-Quentin-Fallavier, France) and then dialyzed at 4 °C against the citrate–phosphate solutions using the Pierce™ 96-well Microdialysis Plate (3.5K MWCO) from Thermo Fisher Scientific (Illkirch-Graffenstaden, France). The ratio of protein to buffer was 1:16 (v/v), at 100 µL of protein solution to 1.6 mL of dialysis buffer. The dialysis buffer was exchanged 3, 6, 16, 19, 22, and 32 h after dialysis began. The protein solutions and dialysis buffers were recovered and sterile-filtered under a laminar flow cabinet using 0.22 µm polyethersulfone filters from Sigma-Aldrich (Saint-Quentin-Fallavier, France). The sdAb solutions were centrifuged for 20 min at 20,000 g and 4 °C and then sterile-filtered as previously described. Protein concentration was determined by measuring absorption at 280 nm using a NanoDropTM 100 from Thermo Fisher Scientific (Illkirch-Graffenstaden, France). The protein solutions were adjusted to 0.5 and 0.2 mg/mL for subsequent biophysical studies.
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7

Quantification of CB2 Receptor Protein

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Samples of plantar paw skin, sciatic nerve and lumbar spinal cord were dissected from euthanized mice, frozen on dry ice, and stored at –80°C until time of processing. Samples of skin and nerve were pooled from both sides of one mouse. On the day of processing, samples were homogenized in a bullet blender in single-detergent lysis buffer (50 mM Tris-HCl, pH 8.0 with 1% Triton X-100, 150 mM NaCl, 0.02% Na azide, 100 μg/ml PMSF, and 1 μg/ml protease inhibitor mixture, Sigma), and the supernatant was obtained after centrifugation at 800 ×g for 10 min. The supernatant was concentrated using an Amicon Ultra-0.5 centrifugal filter (Millipore Corporation, Billerica, MA). Western blot analysis for CB2 receptor protein was performed on 25 μg of protein/sample as previously described [34 (link)] using rabbit anti-CB2 receptor antibody (dilution 1:500, Cayman). Actin immunoreactivity (rabbit anti-actin antibody, 1:2000, Sigma) within each sample was then quantified as a loading control. The density of immunoreactive bands was quantified using ImageJ (version 1.48r 18, NIH). Data for CB2 immunoreactivity were normalized to the amount of actin immunoreactivity within each sample (i.e., density of CB2 /density of actin). The quality of the material used in the analysis is provided in a supplemental figure.
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8

Conditioned Media from GFP+PDGFRα+ Cells Enhances Regeneration

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Conditioned media from GFP+PDGFRα+ cells was obtained by culturing cells as above for 24h in serum free media. Media were collected and gently centrifuged and proteins were concentrated using an Amicon Ultra-0.5 centrifugal filter (Millipore) as described by the Manufacturer. Equal amounts of proteins (approximately 5μg) were injected in 6 mice 24h after HLI induction and the regenerative outcomes were compared to the adoptive transfer of the cells prepared as described above.
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9

Preparation of Targeted Exosomes

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Preparation of TP-Exos was conducted according to the literature [26 (link)] with some modifications. Namely, 3 mg (protein concentration) of purified exosomes dispersed in 900 μl PBS (pH 7.2 - 7.4) was mixed with 100 μg TP dissolved in 100 μl DMSO, and then the mixture was sonicated by an ultrasonic cell crusher (JY92-II, China) (20% power, 15 cycles of a 2 s pulse/2 s pause). After sonication, the mixture was incubated at 37°C for 60 min to allow for recovery of the exosomal membrane. Excess free TP and DMSO were separated from the mixture by centrifugation at 12,000 × g for 30 min using the Amicon Ultra-0.5 Centrifugal Filter (10 kDa, Millipore) and then washed twice with precooled PBS. Finally, the pellet was suspended in PBS, passed through a 0.22 μm syringe filter for sterility, and stored at –80°C until use for studies.
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10

Quantifying NF-kB Activation in Astrocytes

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NF-kB activation was assessed in 6 days differentiated astrocyte-like cells (see above), stimulated, 45 min before being collected, with 10 ng/ml of IL1β in fresh medium.
Proteins were collected by using an extraction kit (Active Motif, Catalog # 40010), according to manufacturer’s instruction. The whole-cell lysates from mNPsc were concentrated by means of Amicon Ultra-0.5 centrifugal filter devices (Millipore) to achieve the recommended concentration of 20 μg of protein per well per sample (20 μl volume). The protein concentration was determined before and after concentration, by the BCA protein assay (Pierce).
NF-kB activation in whole-cell lysates was determined by the TransAM NFkB p65 kit (Active Motif, Catalog # 40096), following the manufacturer’s instructions. This 96 well ELISA-based kit provides colorimetric readout of NF-kB p65 subunit activation, quantified by spectrophotometry at the wavelength of 450 nm (reference wavelength 655 nm). As a positive control for p65 activation, Jurkart nuclear extracts, provided with the kit, were used. Detection limit: <1 μg lysate/well.
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