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251 protocols using ficoll

1

Isolation and Purification of Pancreatic Islets

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The mice were anesthetized with isoflurane, the peritoneum was surged, and the pancreas was removed after injecting collagenase P (Beohringer Mannheim, Germany) into the common the pancreatic duct. The extracted pancreas was incubated for 10 min at 37 °C and effused tissues from the digested pancreas were harvested. The harvested tissues were washed twice with Hank’s balanced salt solution (Gibco, Grand Island, NY, USA) by centrifugation, resuspended evenly in Ficoll (Sigma, St. Louis, MO, USA) with a density of 1.086 g/mL and overlaid with Ficoll at a density of 1.076 and 1.053 g/ml serially. Thereafter, the tube was centrifuged for 10 min at 800× g in a refrigerated centrifuge, and the islets present between the density of 1.076 and 1.053 were collected carefully, washed twice with HBSS, and the pellet was resuspended in M199 (Life Technologies, USA) containing 10% fetal bovine serum culture medium and incubated for 24 h in 5% CO2 incubator at 37 °C. The islets were purified manually under microscope. The purified islets were preserved in liquid nitrogen until subjected total RNA extraction.
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2

Leukocyte Isolation and Cryopreservation

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Samples were centrifuged with Ficoll (Sigma) at 20 °C at 700 × g for 40 min and mononuclear cells were separated by Ficoll gradient to obtain leukocytes. The plasma (first layer) was removed; leukocytes (second layer) were gently washed twice with phosphate-buffered saline (PBS) and centrifuged at 20 °C and 700× g for 15 min. After centrifugation, PBS and dimethyl sulfoxide (DMSO) <0.01 % were added to the samples that were progressively frozen at 10 °C for 30 min, at 20 °C for 30 min, and finally stored at 80 °C until assays were carried out. All samples were evaluated in duplicates.
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3

Assessing Protein Condensate Formation

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Proteins were incubated in 2.5 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT with either 5% Ficoll (Sigma, F2637) for MBP::FUS1 or 15% Ficoll for MBP::IDPC-2 for 1 hr at 30°C with or without TEV protease (10 units in a 50 μL reaction). The optimal percent Ficoll was determined empirically. Turbidity was measure at 395 nm with a Clariostar plate reader (Mandel). 10 μL of each reaction was spotted onto slides with coverslips then condensates visualized with DIC using a Leica DMRA2 microscope at ×63 magnification.
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4

Endothelial Progenitor Cell Isolation and Analysis

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This study was approved by the Institutional Animal Care and Use Committee and the Ethics Committee of Fudan University. Eight-week-old male Sprague-Dawley rats were used for EPC isolation. Bone marrow was isolated from the femur and tibia of the rats and then subjected to density gradient centrifugation using Ficoll (Sigma-Aldrich, #10771). Then, mononuclear cells were cultured on collagen I-coated dishes with EGM-2 medium (Lonza, #CC-3202) at 37°C in a 5% CO2 incubator. After 3 days of incubation, the medium was changed every 3 days. When the cells had reached the second generation, the cells were stained with Dil (Sigma-Aldrich, #42364) and UEA (Sigma-Aldrich, #L9006). Laser confocal microscopy was used for observation of Dil and UEA staining.
The mononuclear cells in the peripheral blood were isolated by Ficoll density gradient centrifugation at 10, 20, or 30 days after the aneurysm model was established. CD34 (Abcam, #ab81289) and KDR (Vascular endothelial growth factor receptor-2, VEGFR-2) (Abcam, #ab9530) monoclonal antibodies were incubated with the mononuclear cells for 1 h on ice and then incubated with Alexa Fluor 546- (ThermoFisher, #A10036) and Alexa Fluor 488-(ThermoFisher, #A11008) labeled fluorescent secondary antibodies for 30 min. The proportion of CD34+/KDR+ cells was analyzed by flow cytometry (Beckman Coulter, DxFLEX).
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5

Perfusion Platform for Capillary Shear Stress

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As described previously32 (link), Ficoll (Sigma Aldrich, St. Louis, MO, USA), was added to EGM-Plus medium at a final concentration of 5% to mimic the viscosity of peripheral blood. To produce shear stress equivalent to that of physiological conditions in vivo (4–23 dyne/cm2), EGM-Plus media supplemented with Ficoll was perfused into the platform through a peristaltic pump. This produced a pressure waveform similar to that seen in capillary beds (2–5 mmHg). The pressure waveform is a function of the peristaltic pump’s roller configuration and rotor speed (rpm). Pump output is a high frequency, low amplitude wave that approximates the capillary bed frequency and pulse pressure. Pressure in the capillary and interstitial compartments reached equilibrium during the acclimation phase of incubation. The platform also has an O-ring to prevent leaks and completely separates the luminal and abluminal chambers. To maintain a stable microenvironment, gas-permeable reservoirs were used to exchange O2 and CO2.
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6

Microinjection of Four-Cell Embryos

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Embryos were microinjected in a 3% Ficoll (w/v; Sigma-Aldrich, St. Louis, MO) solution in 1X MBS on plasticine-coated injection dishes. All embryos were seeded into Ficoll dishes 15 min before injection and allowed to heal for 1 hr in Ficoll after injection. All microinjections were performed at the four-cell stage.
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7

Isolation and Activation of Human T Cells

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Human peripheral T lymphocytes were isolated from whole blood of healthy adult donors by dextran sedimentation and Ficoll (Sigma) gradient separation followed by depletion of B cells using nylon wool column (Unisorb), to which B cells were adsorbed. Cells were incubated in a complete RPMI growth medium (500 ml RPMI Ca/Mg + heat inactivated FCS (10% final) + 5 ml 200 mM L-Glu (2 mM final) +5 ml 100 M Na pyruvate (1 mM final) + 5 ml Pen Strep antibiotics) for more than 2 h, and then non-adherent cells were harvested and transferred to a new plate, resulting in ~90% CD3+ T lymphocytes. Cells were then used for in vitro assay, in which 105 cells were plated per well in a 96-well plate and activated using CD3 and CD28 antibodies.
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8

Synthesis and Characterization of GFc7 Nanocomplex

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GFc7 nanocomplex was synthesized by Sodour Ahrar Shargh Company (Tehran, Iran). Minimum essential medium (α-MEM), penicillin G (100 U/ml), streptomycin (100 μg/ml), GlutaMAX, nonessential amino acids, trypsin-EDTA 0.25 %, and phosphate-buffered solution (PBS) were purchased from Gibco (Gibco-Life Technologies, Carlsbad,CA, USA). Hydrogen peroxide (H2O2), sodium isothiocyanate, dimethyl sulfoxide (DMSO), FeCl3, nitric acid, acetone, methanol and formalin, Triton X-100, beta- glycerol phosphate, NHCl, and paraformaldehyde were purchased from Merck (Darmstadt, Germany). AB-human serum, propidium iodide (PI), hydrocortisone, isobutyl methyl xanthine, indomethacin, Oil Red stain, Alizarin Red stain, dexamethasone, ascorbic acid 2-phosphate, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide 99 % (MTT), p-nitrophenyl phosphate (pNP), Ficoll, and TRIzol were from Sigma-Aldrich (St Louis, MO, USA). IntraStain kit (Code-Nr.K2311) and all of the antibodies were obtained from Dako (Glostrup, Denmark) and Standard SYBR Green PCR kit from Fermentas, St. Leon-Rot, Germany.
The list of the equipment and instruments used is as follows: FACS Calibur (Becton Dickinson, Cockeysville, MD, USA), absorbance micro plate readers (ELx800™; BioTek, Winooski, VT, USA), Rotor Gene 6000 instrument (Corbett, Sydney, Australia), and scanning electron microscope VEGA-TESCAN-LMU model.
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9

PD1-19bbz CAR-T Cell Preparation

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The PD1-19bbz preparation procedure was consistent with our previous report,21 (link) and a summary is presented below. Fresh peripheral blood mononuclear cells (PBMCs) from patients were collected by apheresis. PBMCs were isolated by density gradient centrifugation using Ficoll (Sigma–Aldrich). T cells were enriched through magnetic separation using anti-CD4 and anti-CD8 microbeads (Miltenyi Biotec) and activated with T Cell TransAct (Miltenyi Biotec). T cells were cultured in X-VIVO 15 medium (Lonza) supplemented with CTS Immune Cell Serum Replacement (Thermo Fisher) and recombinant human IL-2 (100 U/mL), IL-7 (5 ng/mL) and IL-15 (5 ng/mL). Cells were collected once cell number reached the requirement for administration and then washed, formulated and cryopreserved. Cell products were shipped to the investigational site after meeting release criteria.
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10

Islet Isolation from Rodent Pancreata

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Islet isolation was performed as described by Schubert et al.34 (link). After euthanasia, a digestion solution containing Collagenase (Sigma-Aldrich, St. Louis, MO, USA) and DNase I (F. Hoffmann-La Roche, Basel, Switzerland) was injected anterogradely into the common bile duct. The pancreata were digested for 15 min., islets were isolated with a discontinuous Ficoll (Sigma-Aldrich) gradient and cultured in RPMI 1640 (Gibco, ThermoScientific, Venlo, Netherlands) supplemented with 10% (vol/vol) FBS (Biochrom). Purity and the amount of islets were determined using dithizone staining (Sigma-Aldrich).
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