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Optiprep

Manufactured by Merck Group
Sourced in United States, Germany, Sao Tome and Principe, Australia, United Kingdom, Canada, Switzerland

OptiPrep is a density gradient media product used for the separation and purification of cells, organelles, and other biological particles. It is a sterile, endotoxin-tested, and non-toxic solution that allows for the density-based separation of various biomolecules and cellular components.

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479 protocols using optiprep

1

Purification of Hepatitis B Surface Antigen

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Hundred milliliter of tetracycline-induced cell culture was centrifuged at 4 °C, 8000 rpm, for 15 min. The cell pellet was either stored at −20 °C until use or immediately resuspended in 10 mL of ice-cold lysis buffer [PBS buffer, 0.6 % (v/v) Tween-20]. Cells were sonicated and the suspension was clarified by centrifugation at 4 °C, 8000 rpm, for 35 min.; the supernatant was left for 16–24 h at RT for particle formation. Subsequently, the lysate was layered on an OptiPrep (Sigma-Aldrich) gradient formed in ultra-clear tubes [2 mL of 30 % (v/v) OptiPrep, 2 mL 24 % (v/v) OptiPrep, 1.5 mL 18 % (v/v) OptiPrep, 1.5 mL 12 % (v/v) OptiPrep, and 1.5 mL 6 % (v/v) OptiPrep in ultra-clear water] and ultracentrifuged at 27,000 rpm for 16 h at 4 °C. Then, 500 µL fractions were harvested and analyzed by western blot using anti-HBsAg rabbit polyclonal antibodies (Abcam). Purity of the fractions was analyzed by SDS-PAGE with Coomassie R-250 staining. sHBsAg positive fractions of the highest purity were pooled, and OptiPrep buffer was replaced with PBS using Amicon Ultra 100 K centrifugal units (Merck Millipore). The thus prepared samples were used for further analysis.
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2

Purification of Hepatitis B Surface Antigen

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Fifty milliliters of the tetracycline-treated cell culture was centrifuged at 4°C at 8,000 rpm for 15 min. The cell pellet was immediately resuspended in 5 mL of ice-cold lysis buffer (PBS buffer, 0.6% [vol/vol] Tween 20). The cells were sonicated, and the suspension was clarified by centrifugation at 4°C at 8,000 rpm for 35 min. The supernatant was left for 16 to 24 h at room temperature (RT) to form particles. Subsequently, the lysate was layered onto an OptiPrep (Sigma-Aldrich) gradient formed in ultraclear tubes (2 mL of 30% [vol/vol] OptiPrep, 2 mL of 24% [vol/vol] OptiPrep, 1.5 mL of 18% [vol/vol] OptiPrep, 1.5 mL of 12% [vol/vol] OptiPrep, and 1.5 mL of 6% [vol/vol] OptiPrep in PBS) and ultracentrifuged at 27,000 rpm for 16 h at 4°C. Next, 500-μL fractions were harvested and analyzed by Western blotting using anti-sHBsAg rabbit polyclonal antibodies (pAbs) (OriGene). The purity of the fractions was analyzed by SDS-PAGE with Coomassie R-250 staining. The fractions with the highest numbers of particles were pooled, and the protein concentration was measured by the Bradford assay (Bio-Rad). Finally, the OptiPrep solution was replaced with PBS using Amicon Ultra 100 kDa MWCO centrifugal units (Merck Millipore). These samples were used for further analysis and immunization.
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3

Isolation and Culture of Neonatal Rat Microglia

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Microglia were isolated from neonatal rat cerebral cortex as described previously (Zhuravleva et al., 2015 ). Briefly, pups were anesthetized and perfused via the left ventricle with cold DPBS solution supplemented with 5 U/ml sodium heparin. The cortex was isolated, and the pia mater peeled off. Tissue was mechanically homogenized and incubated with an enzyme solution (papain 2 mg/ml, DNAse 50 U/ml, dispase 2.5 U/ml) in DPBS for 30 min at 37°C with shaking at 180 rpm. Cells were separated using a 40 μm cell strainer followed by Optiprep (Sigma) discontinuous density gradient for 40 min at 300 g. Layers were cell suspensions in 19% Optiprep, 9% Optiprep, 7% Optiprep, DPBS. A microglia fraction was obtained from a layer, located between fractions 19 and 9%. The microglia were cultured in DMEM/F12 medium supplemented with granulocyte colony-stimulating factor (G-CSF,5 ng/ml, Sigma, United States), 10% FBS, 2 mM L-Glutamine and Penicillin-Streptomycin (PanEco, Russia) in humidified 5% CO2. Resulting cells were transplanted into the area of SCI after 24 h of culture.
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4

Isolation and Purification of HERV-K Virus-Like Particles

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The consensus HERV-K gag/pol gene HERV-Gag-PR-Pol11 (link) was kindly provided by Paul Bieniasz. Transfections were done in HEK293T cells (ECACC) with the consensus HERV-K Gag plasmid using GeneJet as a vessel. The VLPs were harvested 48 h post-transfection by spinning at low speed and filtering the supernatant to remove large cellular debris. The supernatant was then underlayed with 8% OptiPrep (Sigma-Aldrich) in STE buffer (100 mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA; Sigma-Aldrich) as a cushion and spun at 100,000 g, 4 °C for 1:20 h. The pellet was spun onto 10%, 20% and 30% OptiPrep gradient at 120,000 g, 4 °C for 2:30 h. The VLP bands were extracted with a syringe and pelleted again in STE at 160,000 g, 4 °C for 1:20 h to remove residual OptiPrep. The pellet was then resuspended in residual liquid.
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5

Isolation of Pituitary Cell Nuclei

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On the ice, snap-frozen pituitaries were thawed and prepared based on a modified protocol from64 (link). Same-sex samples were processed simultaneously, with all three female samples processed one day, and all three male samples processed another day. Briefly, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 0.1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a Dounce glass homogenizer (1 ml, VWR cat# 71000-514), and the homogenate filtered through a 40 μm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 17,792 × g; 4 C; 25 min). Nuclei were collected from the interphase, washed, resuspended either in 1X nuclei dilution buffer for snATACseq (10 ×  Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted (Invitrogen Countess II).
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6

Isolation of Nuclei from Human Pituitary

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Two methods were tested for nuclei isolation. Frozen post-mortem human pituitaries were either: 1) broken into small pieces in a frozen mortar on dry-ice, and one piece was thawed on ice and prepared for nuclei extraction based on a modified protocol from 44 , or 2) pulverized and part of the powder used for nuclei isolation. The remainder of the pituitary was stored back at -80C. Briefly, and all on ice, RNAse inhibitor (NEB cat# MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl 2 , 3mM Mg(Ac) 2 , 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a Dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 17,792xg; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended either in 1X nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted (Cellometer).
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7

Visualizing Larval Nematodes via Confocal Microscopy

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Worms were on mounted on 2% agarose pads containing 120 mm Optiprep (Sigma Millipore) to reduce refractive index mismatch (Boothe et al. 2017 (link)) on premium microscope slides Superfrost (Thermo Fisher Scientific), and a 22 × 22–1 microscope cover glass (Fisher Scientific) was placed on top of the agarose pad. Worms were anesthetized using a drop of 150 mm sodium azide (Sigma Millipore) with 120 mm Optiprep. Z-stack confocal images of 24 hour old larvae were taken on a Zeiss LSM 880 microscope using a 63X objective lens.
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8

Single-cell RNA-seq of Mouse Cortical Cells

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Dissociated cortical cells were resuspended in PBS, filtered through a 70 micron cell strainer followed by a 40 micron tip strainer, and counted with a Countess instrument (Life Technologies). The cells were further diluted to the final concentration (80,000 cells/mL) with OptiPrep (Sigma) and PBS, and the final concentration of OptiPrep was 15% vol/vol. A total of 2,000 to 5,000 cortical cells were collected per mouse and processed following the InDrop protocol [38 (link),110 (link)]. Final libraries containing ~1,200 cells were constructed and sequenced on an Illumina NextSeq 500 instrument, generating on average ~130 million reads per library (S3 Table).
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9

Cardiac Nuclei Isolation and Enrichment

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Nuclear isolation was performed as previously described, with the following specifications (Mo et al., 2015 (link)): Briefly, fresh cardiac tissue was harvested on ice and was immediately homogenized with a Biogen Series PRO200 (PRO Scientific) before performing Dounce homogenization in HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH 7.8; with protease inhibitors; 1mM DTT; 0.15mM Spermine; 0.5mM Spermidine, and RNAse inhibitors) with 5% IGEPAL CA-630. Nuclei were isolated via density gradient centrifugation with optiprep density gradient medium after mixing homogenate 1:1 with a 50 iodoxinal (5 volumes optiprep [Sigma-Aldrich, Cat#D1556] with 1 volume Diluent [150mM KCl; 30mM MgCl2; 120mM Tricine-KOH; pH 7.8]) . After 18 minute 10,000G centrifugation, all nuclei isolated from a 30% to 40% interface were precleared with Protein-G Dynabeads (Thermo Fisher Scientific, Cat#10004D). Next, nuclei were immunoprecipitated with an anti–PCM-1 (Sigma-Aldrich, Cat#HPA023370) antibody and Protein-G Dynabeads (washing 7 times with Buffer HB with 0.4% IGEPAL CA-630 ) to enrich for CM nuclei as described previously (Gilsbach et al., 2014 ).
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10

Propagation and Purification of Recombinant Vesicular Stomatitis Virus

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VSVΔ51-Fluc: The Indiana serotype of VSV used throughout this study was propagated in Vero cells and purified on 5-50% Optiprep (Sigma-Aldrich, St. Louis, MO). VSVΔ51 expressing firefly luciferase are recombinant derivatives of VSVΔ51 described previously (10 (link)).
VSVΔ51 encoding/expressing IL-12: VSVΔ51 encoding/expressing IL-12 was generated in the laboratory of Dr. Rebecca Auer using PCR amplified from pORF-mIL12 [IL12elasti(p35:p40); In vivoGen] (20 (link)). Virus was produced and purified on 5-50% Optiprep (Sigma-Aldrich, St. Louis, MO) in our laboratory.
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