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438 protocols using mineral oil

1

HER2-Binding Protein Library Selection

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In vitro transcription and translation were performed as previously described (Houlihan et al., 2014 (link)). Briefly, 5 ng of DNA were added to the in vitro transcription and translation (IVTT) mix [PURExpress, NEB (Kanamori et al., 2014 (link))], then homogenised in ice-cold mineral oil mix [95% mineral oil (Sigma-Aldrich), 4.5% Span 80 (w/w) (Fluka), 0.5% Tween 80 (w/w) (Sigma)]. The emulsion was incubated at 25°C for 4 h, then the aqueous phase extracted in recovery and binding buffer [phosphate buffered saline (PBS) supplemented with 5 mM EDTA and 10 μM BG]. The displayed protein library was incubated with biotinylated HER2 (purchased from R&D Systems, cat. no. 1129-ER-050) and captured on streptavidin-coated beads (Dynal). Biotinylation of HER2 was performed as described in Houlihan et al. (2014) (link). After incubation for 1 h, streptavidin beads were washed (five times with PBS supplemented with Tween 20, 0.01% v/v) and remaining HER2-bound DARPins were eluted with KOH (6 mM). Recovered DNA was amplified using the primers sel-fwd (5′-TTGGGAGGTACCGGCGGTCTG-3′) and sel-rev (5′-GTTAGCAGCCGGATCCTCACTATAAC-3′) and reassembled as described above. DNA was purified using QIAquick PCR purification kit (QIAgen), precipitated with PEG-MgCl2 and used in the following round of selection or cloned into pQE30 for sequencing.
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2

Chronic Odorant Stimulation in Mecp2 Mice

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M71 or M72 mouse pups (Mecp2 WT or KO littermates) were raised with or without odorant stimulation. Control group was treated with mineral oil (Sigma) and odorant group with 1% acetophenone (Sigma) diluted in mineral oil. Chronic odorant stimulation was conducted by applying 1% acetophenone daily to the beddings and the nipples of the lactating mother. The treatments started at P1 (postnatal day 1) and continued until the mice were sacrificed at P14, P28 or P49. For acute stimulation of odorant, Mecp2WT and KO mice were exposed to a mixture of 3 odorants at concentrations that we previously described (Moon et al., 1999 (link)). Six to eight weeks old male WT and KO mice were used for acute odorant treatment.
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3

Measuring Enteroid Luminal Volume

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Enteroids at day 3 of culture were treated with 1 μM Rh123 (Sigma-Aldrich) for 180 min at 37 °C and 1 μm Z-stack images were acquired. The luminal volume of enteroid was measured as accumulated Rh123 in enteroid lumen using by 3D measurement tool in NIS-elements AR. For measurement of injection volume, fluorescein and mineral oil (Sigma-Aldrich) were loaded into the needle in the order and the diameters of the interface between fluorescein and mineral oil before and after microinjection and moving distance by microinjection were measured.
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4

Synthesis and Characterization of GelMA

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In order to synthesize GelMA, dimethyl sulfoxide (Sigma Aldrich, St. Louis, MO, USA) was mixed with 5 g of gelatin (Sigma Aldrich, St. Louis, MO, USA). The mixture was heated up to 50 °C with continuous stirring. After 0.5 g of 4-(dimethlyamino)-pyridine (Sigma Aldrich, St. Louis, MO, USA) was dissolved with the solution, 2 mL of glycidyl methacrylate (Sigma Aldrich, St. Louis, MO, USA) was added to the solution at a constant flow rate of 0.5 mL/min with vigorous stirring. The reaction was kept for two days under a dry N2 gas environment. And the solution was filtered using a membrane (molecular weight 12,000 to 14,000) with deionized water at 40 °C for 1 week. The deionized water was replaced once a day. A lyophilization-induced aggregated porous solid was obtained and stored at −80 °C. GelMA prepolymer solutions at 3 wt%, 5 wt%, and 8 wt% were prepared. Sodium alginate (Sigma Aldrich, St. Louis, MO, USA) with an average molecular weight between 12,000 and 40,000 was dissolved in deionized water to prepare concentrations of 0.1 wt%, 0.3 wt%, 0.5 wt%, 0.7 wt%, and 1 wt%, respectively. Mineral oil (Sigma Aldrich, St. Louis, MO, USA) and 25 wt% of Span 80 (Sigma Aldrich, St. Louis, MO, USA) were purchased and mixed together to increase the viscosity of the Mineral oil for emulsification.
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5

Vascular Permeability Measurement in Rats

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TIE-1-Igγ1-WT, 2-16A2 or ASP4021 diluted with PBS was subcutaneously administered to SD rats. At 48 h after administration of the antibody, Evans Blue dye dissolved in physiological saline (Sigma) was intravenously administered. Immediately, 20 μl of allyl isothiocyanate (also known as mustard oil; Nacalai Tesque) diluted with 5% mineral oil (Sigma) was applied to one ear, and mineral oil to the contralateral ear. After 30 min, both ears were sampled, weighed, then immersed in 1 mL of formamide, and incubated at 70 °C overnight to extract Evans Blue dye from the ear tissue. The Evans Blue dye concentration was determined from the absorbance (measurement wavelength of 620 nm and control wavelength of 740 nm) of the extract. The amount of leakage per ear weight was calculated by dividing the Evans Blue dye concentration by the weight of the ear. The final amount of leaked Evans Blue dye from each animal was calculated by subtracting the amount of leaked Evans Blue dye from the ear that received mineral oil from the amount from the ear that received mustard oil in the same animal. The amount of leaked Evans Blue dye was used as an index of vascular permeability.
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6

Stereotaxic Surgery for Rat dLGN Recording

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Rats were pre-anaesthetised with isoflurane (3%, Aerrane; Baxter, Poland; v/v air mixture) in an induction chamber for 10 min. During stereotaxic surgery and recording procedures, a mixture of 2-3% (300 ml/min air) isoflurane, 30% O2 and 70% N2O was delivered via an anaesthetic mask (Kopf Instruments, Tujunga, USA). The electrocorticogram (ECoG) and body temperature (~37°C) of the rats were monitored during the recording procedures. Each animal's head was held in a stereotaxic frame (Advanced Stereotaxic Instruments, USA), and the skull was exposed via a midline scalp incision. Bregma and lambda reference points were determined, and a craniotomy was performed above the dLGN with the use of the rat stereotaxic brain atlas (Paxinos and Watson, 2007) . The following coordinates were used: 4.5-4.9 mm posterior, 3.6-4.2 mm lateral to the bregma and 4-4.7 mm ventral from the surface of the cortex. The dura was nicked with a fine needle, and a small drop of mineral oil (Sigma-Aldrich, Poland) was applied to the exposed brain surface. The pupil of the stimulated eye was dilated with atropine (Atropinum Sulfuricum WZF 1%, Polfa, Poland), and mineral oil (Sigma-Aldrich, Poland) was applied to retain corneal moisture.
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7

Quantification of Calcium Deposition in Osteogenic DPSCs

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Alizarin red S is a calcium-sensing dye. DPSCs, differentiated towards the osteogenic phenotype, are able to deposit and to induce the mineralization of extracellular matrix rich in calcium phosphate, which can be identified by Alizarin red S. Calcium deposits are detectable for their bright orange-red color.
The DPSCs in each well were rinsed twice with PBS, PBS was discarded and DPSCs were fixed in paraformaldehyde 4% for 15 min at room temperature and then washed with deionized water. Alizarin red S staining solution 40 mM (Merck KGaA, Darmstadt, Germany) was added to each well and probed for 20 min at room temperature (RT) on a shaker. The wells were washed for five times in deionized water. Calcium deposits, stained in orange-red, were dissolved as follows: 10% acetic acid was added under shaking for 30 min. Laminas were scraped, the liquid containing deposits was collected and vortexed in a tube. Previously heated warm mineral oil (Merck KGaA, Darmstadt, Germany) was added, the tube maintained on ice for 5 min and eventually centrifuged at 20,000 g for 15 min. The supernatant was discarded and 10% ammonium hydroxide (Merck KGaA, Darmstadt, Germany) was added. The final solution was analyzed by a spectrophotometric reading performed at 405 nm wavelength.
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8

Inducible Genetic Manipulation in Mice

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Housing of mice and in vivo experiments were performed in compliance with the European Communities Council Directive of 24, November 1986 (86/609/EEC) and national and institutional guidelines. Animal care and experimental procedures were approved by the Animal Care Committee of the Institute of Molecular Genetics (ref. 58/2017). ApccKO/cKO mice [41 (link)] were obtained from the Mouse Repository (National Cancer Institute, Frederick, MD, USA); Villin-CreERT2 mice [42 (link)] were kindly provided by Sylvie Robine (Institut Curie, Centre de Recherche, Paris, France); Apc+/Min (C57BL/6J-ApcMin/J) [43 (link)], Ki67-RFP (Mki67tm1.1Cle/J) [44 (link)], Lgr5-EGFP-IRES-CreERT2 (B6.129P2-Lgr5tm1(cre/ERT2)Cle/J) [45 (link)], and Rosa26-tdTomato (B6;129S6-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J) [46 (link)] mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). The animals were kept under specific pathogen-free conditions. To induce Cre-mediated gene recombination, mice were gavaged with 1 mg tamoxifen (Merck). tamoxifen was dissolved in ethanol (100 mg/mL) and combined (1:9) with mineral oil (Merck) before administration. Mice were sacrificed by cervical dislocation at various time points after administration of a single dose (100 µL) of the tamoxifen/oil solution.
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9

Antioxidant Activity Analysis of Foodstuffs

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All reagents were of analytical grade. Graphite powder, copper chloride, potassium ferrocyanide and all phenolic standards were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA). Mineral oil and the electrolyte buffer salts were purchased from Merck (Darmstadt, Germany).
Foodstuffs samples with known antioxidant activity were purchased from local markets and drugstores of the city of Goiânia, Goiás, Brazil.
Assay samples were prepared by sonication in ethanol:buffer (1:1) solution in order to achieve a 10% final concentration. Standards were prepared in suitable solvents in order to get stock solutions of 10 mM final concentration.
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10

3D Cell Culture Imaging and Tracking Protocol

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Cells were grown in glass chambers (Thermo Fisher Scientific). At 1 h before imaging, the medium was changed to pre‐warmed Leibovitz's L‐15 medium (Thermo Fisher Scientific) supplemented with 20% FBS and 20 mM HEPES, pH 7.0. In 3D culture conditions, spheroid cultured cells were dropped into a 3.5‐cm glass‐bottomed dish (MatTek Corporation) with REBM supplemented with B‐27 Supplement, N‐2 supplement, and 10 μM ROCK inhibitor Y‐27632, and covered with mineral oil (Merck). The dish was coated with 0.5% poly(2‐hydroxyethyl methacrylate) (Merck) in 95% ethanol before cell seeding for 24 h. Cells were treated with SiR‐DNA (Spirochrome) for 6 h before imaging. Recordings were made at 37°C, as described previously.25, 26, 27, 28, 29 Z‐series of three sections in 3‐μm increments were captured every 3 min. Image stacks were projected. Images were collected with an Olympus IX‐71 inverted microscope controlled by DeltaVision softWoRx (Cytiva) using a ×20 0.75 NA UPlanSApo objective lens (Olympus). All cells were tracked using the ImageJ program with the plug‐in TrackMate.30
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