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92 protocols using tls 55 rotor

1

Sucrose Density Gradient Fractionation of Detergent-Resistant Membranes

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6.5 × 107 human PBMC were treated with 40 μM of hTip-CSKH in serum-free RMPI-1640 during 1 hour at 37°C. The cells were washed in medium and the membranes were extracted during 20 min in 200 μL of ice-cold lysis buffer containing Tris 25 mM pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.5% Triton-X100, 1 ug/mL leupeptin, 1 ug/mL pepstatin, 4 ug/mL aprotinin, 1 mM PMSF, 1 mM Na3VO4, and 50 mM NaF. For sucrose density gradients, cell extracts were mixed with 250 μL of 80% sucrose in TNE buffer (Tris 25 mM pH 7.4, 150 mM NaCl, and 2 mM EDTA) and overlayed with 730 μL of 35% sucrose and 320 μL 5% sucrose and centrifuged at 200,000 g during 5 h, 4°C (Beckman Optima, rotor TLS-55). Eight fractions of equal volume were recovered from the top of the gradient, diluted with 1 mL of TNE, and detergent resistant membranes in each fraction were precipitated by ultracentrifugation at 100,000 g during 45 min, 4°C. The pellets were extracted in 20 μL of Laemmli buffer: half used for WB and Flotillin-2 detection and the other half for SDS-PAGE in Tris-Tricine buffer for peptide identification as described [42 (link)]. To facilitate the identification of the peptides in this system, erythrocyte membranes were prepared in parallel and incubated with the different peptides used. Peptides were identified by sample separation in Tris-Tricine SDS-PAGE.
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2

Microsomes Separation by Percoll Gradient

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Thirty percent Percoll was prepared from a 100% Percoll solution by mixing 100% Percoll with 1xPBS at a ratio of 3:7 (volume). A total of 2 mL of the 30% Percoll solution was pipetted into a centrifugation tube. Total microsomes (P100k) resuspended in PBS or samples eluted from the immunoprecipitated beads (200 μL) were carefully layered on top of the Percoll solution. Centrifugation was performed at 95,000 x g (rotor TLS55, Beckman) at 4°C for 40 min. After centrifugation, the gradient was fractionated into 21 tubes, 100 μL per fraction. The samples were then analyzed by Western blotting and quantified with ImageJ.
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3

Nuclear Protein Complex Analysis via Sucrose Gradient

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Sucrose gradient sedimentation analysis was performed as described39 (link). Briefly, 10–40% gradients were formed by layering 500 µl NEB1 buffer containing 10%, 20%, 30%, or 40% sucrose in a 11 × 34-mm centrifuge tube (Beckman) and allowed to equilibrate at room temperature for 2 h. Gradients were chilled, loaded with 500 µg MCF7 nuclear extract (adjusted to a volume of 150 µl) or 150 µl molecular weight markers (Sigma MW-GF-1000), and centrifuged in a Beckman TLS-55 rotor at 50,000 rpm (214,000×g) for 14 h. Thirty-six fractions of •45 µl were collected. For the markers, 20 µl of each fraction was electrophoresed and Coomassie stained. For the gradient fractions, 20 µl of fractions were analysed by immunoblotting using EZH2 (Cell Signaling Technology), SUZ12 (Abcam ab12073), TRIM37 (Abcam), RNF2 (Abcam ab101273) and BMI1 (Bethyl Laboratories, A301-694A).
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4

Nuclear Protein Complex Analysis via Sucrose Gradient

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Sucrose gradient sedimentation analysis was performed as described39 (link). Briefly, 10–40% gradients were formed by layering 500 µl NEB1 buffer containing 10%, 20%, 30%, or 40% sucrose in a 11 × 34-mm centrifuge tube (Beckman) and allowed to equilibrate at room temperature for 2 h. Gradients were chilled, loaded with 500 µg MCF7 nuclear extract (adjusted to a volume of 150 µl) or 150 µl molecular weight markers (Sigma MW-GF-1000), and centrifuged in a Beckman TLS-55 rotor at 50,000 rpm (214,000×g) for 14 h. Thirty-six fractions of •45 µl were collected. For the markers, 20 µl of each fraction was electrophoresed and Coomassie stained. For the gradient fractions, 20 µl of fractions were analysed by immunoblotting using EZH2 (Cell Signaling Technology), SUZ12 (Abcam ab12073), TRIM37 (Abcam), RNF2 (Abcam ab101273) and BMI1 (Bethyl Laboratories, A301-694A).
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5

SUV Integrin Separation by Sucrose Gradient

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For SUV visualization on sucrose gradient, 0.5% (w/w) of rhodamine
DHPE was added to the lipid composition of α5β1 integrin/SUVs, prepared, as described above. In a cold room,
100 μL of α5β1 integrin/SUVs
were diluted to a final volume of 575 μL in 20 mM HEPES, 150
mM NaCl, 30% (w/v) sucrose, pH 7.4, and placed at the bottom of a
2.5 mL polypropylene ultra-centrifuge tube. Sucrose gradient was then
built by gently pouring, from the bottom to the top of the tube, 575
μL of 20, 10, 5, and 0% (w/w) sucrose solutions prepared in
20 mM HEPES and 150 mM NaCl pH 7.4 buffer. The sample was centrifuged
at 100,000×g (Beckman TLS55 rotor) for 16 h
at 4 °C. Samples were collected from each sucrose density, denatured
in non-reducing SDS-sample loading buffer, boiled for 5 min, and loaded
on a 4–15% pre-casted polyacrylamide gel. Proteins were then
transferred on the nitrocellulose membrane, and the presence of α5β1 integrin in all fractions was immuno-detected
by incubation with primary hamster anti-rat β1 integrin
antibodies, followed by secondary HRP-coupled anti-hamster antibody.
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6

Reconstitution of Replisome Assembly

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Replisome assembly reactions were set up to yield a final volume of 10 μl containing: 150 nM CMG with a 1.5-fold molar excess of fork DNA1 (link), TIM–TIPIN, CLASPIN, AND-1, Polε, CTF18–RFC in reconstitution buffer (25 mM HEPES-NaOH (pH 7.6), 150 mM NaOAc, 0.5 mM TCEP, 500 μM AMP-PNP and 10 mM Mg(OAc)2). CMG (or CMG storage buffer in the –CMG reaction) was first incubated with fork DNA1 (link) for 15 min on ice.
Next, the remaining proteins were added and the final volume was adjusted to 10 μl. The reaction was loaded onto a 230 μl 10–30% glycerol gradient in a buffer containing 40 mM HEPES-NaOH (pH 7.5), 150 mM NaOAc, 0.5 mM TCEP, 500 μM AMP-PNP and 3 mM Mg(OAc)2. Samples were separated by centrifugation (Beckman TLS-55 rotor; 200,000g at 4 °C for 1 h). Fractions (10 μl) were collected manually and analysed by 4–12% SDS–PAGE with silver staining (Invitrogen). For the Polα–CMG gradient, 100 nM CMG was mixed with 80 nM Polα in reconstitution buffer for a final volume of 10 μl and incubated on ice for 30 min. The reaction was loaded onto the gradient and fractions were analysed as described above.
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7

Separation of Amyloid-beta Assemblies

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In order to separate differently sized Aβ1–42 assemblies, 100 μl of the sample were added on the top of a discontinuous gradient of iodixanol (OptiPrep, AXIS-SHIELD, Oslo, Norway). The gradient was prepared by layering 260 μl of 50% iodixanol at the bottom of a 11 x 34 mm polyallomer centrifuge tube, overlaid by 260 μl of 40%, 260 μl of 30%, 780 μl of 20%, 260 μl of 10% and 100 μl of 5% iodixanol. The samples were spun at 260,000 x g for three hours at 4°C in an Optima MAX-XP ultracentrifuge with a TLS-55 rotor (both Beckman Instruments, Brea, USA). After centrifugation, 14 fractions of 140 μl each were harvested with a pipette from top to bottom.
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8

Sucrose Gradient Isolation of γ-TuRC

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Sucrose was dissolved in CSF-XB buffer (without sucrose) to prepare light and heavy solutions (10–50% or 15–45% [wt/vol]). Continuous sucrose gradient was made by mixing the two solutions using Gradient Master (Biocomp). After loading samples, differential centrifugation was performed using TLS-55 rotor (Beckman Coulter) at 200,000 g for 4 h at 4°C. Samples were fractionated and loaded on SDS-PAGE gels, followed by Western blot analyses to determine γ-TuRC containing fractions.
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9

Sucrose Gradient Fractionation of LUVs-VPS34

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The mixture of proteins and lipids contained 1.8 mM (~1.5 mg/mL) LUVs and 2 μM VPS34 complex in buffer containing 25 mM HEPES pH 8.0, 150 mM NaCl and 1 mM TCEP. The total sample volume was 20 μL. While the LUVs and proteins were incubated on ice for 30 min, a sucrose gradient was prepared. For the gradient, several sucrose solutions were layered from the bottom to the top in a Beckman centrifuge tube (343775 Thickwall Polycarbonate Tube, Beckman Coulter): 40 μL 30% sucrose solution, 52 μL 25% sucrose solution, 52 μL 20% sucrose solution. Then 16 μL of the LUV/protein sample was carefully pipetted on top of the gradient. From the remaining LUV/protein sample, 2.5 μL were kept as an input sample for the SDS-PAGE. The gradient was then centrifuged for 3 h in a TLS-55 rotor (Beckman Coulter) at 258,500 × g at 4 °C. Afterwards, 6 fractions of 26 μL each were carefully collected from the top of the gradient. The input and gradient fractions were analysed by SDS-PAGE.
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10

Lipid Raft Isolation and Analysis

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Lipid rafts were isolated as described previously [11 (link)]. Briefly, 3 × 107 N2a-WT cells treated for 3 days with EFV (20 µM) or not were solubilized in 400 μl cold lysis buffer (NaCl 150 mM, Tris–HCl pH 7.5 25 mM, EDTA 5 mM, and Triton-X 100 1%) and incubated on ice in the cold room for 30 min. The cell lysates were mixed with Nycodenz 70% in TNE (NaCl 150 mM, Tris–HCl pH 7.5 25 mM, EDTA 5 mM) to a final concentration of 35% Nycodenz and were overlaid by 200-μl fractions of Nycodenz solutions with concentrations of 25, 22.5, 20, 18, 15, 12, and 8%. After ultracentrifugation (200,000 g, 4 h, 4 °C, Beckmann TLS55 rotor), fractions were collected from the top to the bottom of the gradient and precipitated with methanol for immunoblot analysis.
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