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137 protocols using paraformaldehyde (pfa)

1

Flow Cytometric Analysis of Cell Populations

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Organs were digested by collagenase (Sigma, C2674) in 37 °C for about 1 hour to be disrupted into single cells. Flow cytometric cell sorting was performed using Beckman coulter (gallios). Hematopoietic cells were excluded by sorting with negative CD45 (Biolegend, 103106) and negative Ter119 (BD Biosciences, 563995). DCFH-DA (Thermo Fisher Scientific, D399) and Mitotracker deep red (Thermo Fisher Scientific, M22426) were stained for flow cytometric analysis according to the manufacturer’s instructions. γ-H2AX antibody was stained for flow cytometery after fixation and permeabilization by 4% PFA (Sinopharm chemical reagent, 80096628) and 0.1% saponin (Sigma, 47036). Apoptosis and necrosis were analyzed with flow cytometry by double staining of annexinV and PI (BD Biosciences, 556419) following manufacturer’s instructions. Thymus T cells and NK cells were analyzed with antibodies against in combinations of CD4 (BD Biosicences, 553049) and CD8 (Biolegend, 100706), or CD3 (eBioscience, 11-0032-82) and NK1.1 (Thermo Fisher Scientific, MM6628).
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2

Synthesis and Characterization of Disulfide Compound

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PFA, acetone, anhydrous ethanol, chloroform, tetrahydrofuran (THF), N-methyl-2-pyrrolidone (NMP), dimethyformamide (DMF), hydrochloric acid (HCl, 36%), and sodium hydroxide (NaOH) were purchased from Sinopharm Chemical Reagent Co., Ltd., Shanghai, China. 4-aminophenyl disulfide and 2-mercaptoethanol were purchased from Shanghai Taitan Technology Co., Ltd., Shanghai, China. All the chemicals were used as received without further purification.
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3

Quantifying Brain Atrophy After Stroke

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Mice were sacrificed at 14 and 28 days after tMCAO, and brain atrophy volume was examined as described before 45 (link). Briefly, brain tissues were sequentially immersed in 4% paraformaldehyde (PFA, Sinopharm Chemical Reagent, Shanghai, CN) and 30% sugar solution at 4°C after cardiac perfusion of PBS and 4% PFA. The mouse brain was cut into 30 μm coronal sections from the anterior commissure to the hippocampus. Brain slices (300 μm apart) were stained with 0.05% Cresyl violet acetate (Sigma-Aldrich), the area of the contralateral and the ipsilateral hemisphere was measured using Image J software (NIH, Bethesda, MD). The atrophy area denoted as ∆S was calculated by subtracting ipsilateral area from contralateral area. The thickness between two adjacent brain slices was described as height (H), and the atrophy area of two adjacent slices was denoted as ∆Sn and ∆Sn+1. Total brain atrophy volume was then calculated according to the formula: V= ∑H/3×[∆Sn+(∆Sn×∆Sn+1)1/2+∆Sn+1].
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4

Histological Analysis of Kidney

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The kidneys were fixed in 4% PFA (30,525–89-4, Sinopharm, Shanghai, China), dehydrated, and embedded in paraffin. The paraffin-embedded tissues were cut into sections of 5 μm thickness. The sections were dewaxed and subjected to hematoxylin (CTS-1099, MXBio, Fuzhou, China) and 0.5% eosin (71,014,544, Sinopharm). Subsequently, slices were mounted with neutral gum (G8590; MAIRUI, Shanghai, China). Images of glomerular and mesangial membrane morphologies were observed under a microscope.
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5

GdCl3 and Apyrase Assay Protocol

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GdCl3 (Sinopharm Chemical Reagent Company, Beijing, China), ruthenium red (RuR) (Sigma-Aldrich, St. Louis, MO, USA), 6-N,N-Diethyl-β-γ-dibromomethylene-D-adenosine-5′-triphosphatetrisodium salthydrate (ARL67156) (Sigma-Aldrich, St. Louis, MO, USA) and apyrase (Sigma-Aldrich, St. Louis, MO, USA) were prepared with distilled water. 2-Methyl-1-[3-(4-morpholinyl)propyl]-5-phenyl-N-[3-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxamide (HC067047) (Tocris, Minneapolis, MN, USA) was dissolved in dimethyl sulfoxide (DMSO). All of these stock solutions were kept at −20 °C and diluted into working solutions to final concentrations when used. DMSO was kept at less than 0.1% in the final solution. Finally, 4% paraformaldehyde (PFA) (Sinopharm Chemical Reagent Company, Beijing, China) was prepared in a fume hood and stored at 4 °C.
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6

Brain Tissue Collection and Processing

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Mice were euthanized with 5% isoflurane and sacrificed at corresponding timepoints post-operation by cervical dislocation. For western blot and quantitative real-time polymerase chain reaction (qPCR), brains were removed and the tissue in striatum adjacent to the hematoma or the corresponding part in sham group (about 60 mg) was isolated and stored at -80°C until processing.
For immunohistochemistry and immunofluorescence, mice were transcardially perfused with 0.9% saline, followed by 250 mL ice-cold 4% paraformaldehyde (PFA; Sinopharm Chemical Reagent Co., Ltd., Shanghai, China) in 0.1 M phosphate buffer (PBS, pH = 7.4) after anesthetized with chloral hydrate. The fixed brains were removed and post-fixed in 4% PFA for 24 h (4°C) and then gradually dehydrated in 20% and 30% sucrose in PBS (pH = 7.4, 4°C). Coronal slices of 30 μm were performed at -20°C using a constant temperature freezing microtome (CM 1860, Leica, Wetzlar, Germany). They were then gently transferred to the microslides and stored at -80°C until processing.
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7

Histopathological Analysis of Arteriovenous Anastomosis

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One part of the vascular tissue from the arteriovenous anastomosis site was fixed in 4% paraformaldehyde (China National Pharmaceutical Group Corporation, Shanghai, China) for 24 h and embedded in paraffin. Then, 5 μm sections were cut. Some of the sections were stained with hematoxylin-eosin (HE) for histopathological examination, and the other sections were used for IHC staining. For IHC staining [16 (link)], the sections were dewaxed, rehydrated, and subjected to antigen retrieval. After blocking endogenous peroxidase activity, the samples were, respectively, incubated with anti-CD31 antibody (1 : 200, Wuhan Servicebio Co. Ltd, Wuhan, China) at 4°C overnight. After washing three times with PBST, the samples were incubated with horseradish enzyme-labeled secondary antibody (1 : 200, cat. no. G1215-3, Servicebio) at 37°C for 30 min. After washing, the sections were stained with diaminobenzidine (DAB) for 1 min and stained with hematoxylin for 30 s. After dehydration and sealing, the slides were scanned and images were taken under an optical microscope (Olympus Corporation, Tokyo, Japan) at 400x magnification.
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8

Brain Tissue Sampling and Histopathology Analysis

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The rats were sacrificed after being anaesthetized, and the brain tissues were collected. One part of the brain tissues was fixed with 4% paraformaldehyde (China National Pharmaceutical Group Corporation, Shanghai, China) for histopathology examination. The other part was washed in sterile phosphate buffer saline (PBS), frozen in liquid nitrogen, and stored at −80°C for subsequent studies.
The method of histopathology analysis was described previously [18 (link)]. In brief, the brain tissues were fixed in 4% paraformaldehyde and embedded in paraffin. The 5 μm sections were cut and stained with haematoxylin-eosin (HE). Slides were scanned, and images were taken under optical microscopy (Olympus Corporation, Tokyo, Japan). The histopathological scoring criteria are shown in Table 1 [19 (link)].
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9

Histological Analysis of Fixed LV

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The isolated LV was fixed with 4% paraformaldehyde (China National Pharmaceutical Group Corporation, Beijing, China), embedded in paraffin, and sectioned to a thickness of 4 μm with a microtome (Leica RM2265, Wetztlar, Germany). After dewaxing, sections were stained with hematoxylin-eosin or Picro Sirius Red. Cell area and collagen fiber area were analyzed by ImageJ software.
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10

Rat Brain Tissue Preparation Protocol

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After 2 months of modeling, all rats were generally anesthetized with a combination of sodium pentobarbital intraperitoneal injection (50 mg/kg, China National Pharmaceutical Corporation) and isoflurane inhalation (2%), the process complied with the applicable veterinary guidelines (such as the American Veterinary Medical Association). Thereafter, the rats were intubated to the renal aorta through the left ventricle via a thoracotomy; blood samples were extracted using an EDTA tube and were preserved. Following this, 30 mL of normal saline was injected through a catheter, while the vena cava was cut open to drain the blood. Three rats were slowly injected through a catheter with 120 mL of 4% paraformaldehyde (China National Pharmaceutical Group Corporation)/0.1 M phosphoric acid buffer (pH 7.4, China National Pharmaceutical Group Corporation) for fixation; the other rats remained without this treatment. Thereafter, cervical dislocation was applied to kill the rats, and their brains were removed via craniotomy. The circle of Willis of each brain was carefully separated under a 10–16× surgical microscope. Among them, the three fixed circle of Willis samples were subjected to hematoxylin and eosin (HE) staining; the remaining five and blood samples were used to isolate the total RNA using the Trizol method.
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