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Eb dye

Manufactured by Merck Group
Sourced in United States, Sao Tome and Principe, United Kingdom

EB dye is a fluorescent compound used in molecular biology and biochemistry applications. It binds to nucleic acids, such as DNA and RNA, and emits an orange-red fluorescence when exposed to ultraviolet or blue light. The core function of EB dye is to enable the visualization and detection of nucleic acids in various lab techniques, such as gel electrophoresis and fluorescence microscopy.

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41 protocols using eb dye

1

BBB Permeability Evaluation by EB Dye Extravasation

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As reported, BBB permeability was evaluated by EB dye extravasation assay.15 Briefly, 4% EB dye (4 mL/kg, Sigma‐Aldrich) was injected intraperitoneally at 3 h before sacrifice evaluation, and mice were sacrificed 24 h after ICH. The right hemisphere was homogenized and sonicated within 1100 μL PBS and then centrifuged for 30 min at 15,000 g. 500 μL supernatant from each sample was mixed with 500 μL 50% trichloroacetic acid overnight at 4°C. After centrifugation, the supernatant was collected, and EB dye extravasation was evaluated at 610 nm and quantified according to a standard curve.
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2

Quantifying Blood-Spinal Cord Barrier Integrity

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The evaluation of BSCB integrity was performed with quantitative and qualitative measurements of EB extravasation and spinal cord edema. The content and fluorescence of EB were examined. Briefly, 60 min after the injection of EB dye (20 g/L; Sigma) at a dose of 10 ml/kg via the tail vein, the animals were anesthetized and then transcardially perfused with 0.9% saline containing 10 IU/ml heparin, until colorless perfusion fluid was obtained from the right atrium, to remove all EB dye that had not leaked into the interstitium. The L4–6 spinal cord tissue was weighed, then soaked with methanamide for 24 h (60 °C) and centrifuged. The fluorescent absorption of the supernatant was detected at 632 nm with a microplate reader (BioTek, Winooski, USA) and presented as EB amount per tissue weight (μg/g) with standardized curve. Furthermore, the spinal cord tissue was fixed with 4% paraformaldehyde. The transverse sections (10 μm) were visualized under a BX-61 (Olympus, JP) fluorescence microscope. EB dye was visualized as red under the green fluorescence excitation mode. The integrated optical density (IOD) of the positive fluorescence labeling in the lumbar spinal cord tissue was analyzed to quantify the EB extravasation (Image Pro Plus 6.0). The percentage of water content in the spinal cord tissue was calculated with a wet-dry method: (wet weight − dry weight)/wet weight × 100.
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3

Brain Permeability Assay for PDGF-CC

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For BBB permeability analysis active PDGF-CC core protein (3 μM) or PBS as control was ICV injected into the dorsal 3rd ventricle (bregma-0.94, mediolateral 0 and dorsoventral-2.45) in mice pre-treated with either imatinib (or PBS as control) or 6B3 antibody (or BM4 as control) 2-5 h before ICV injection. Directly after ICV injection mice were intravenously injected with 0.1 ml of 4% EB dye (Sigma-Aldrich). 2 h later, animals were perfused with HBSS for 8 min and the brains were removed and photographed with a Samsung s4mini mobile phone (Samsung, South Korea). Each brain was then homogenized in N,N-dimethylformamide (Sigma-Aldrich) and centrifuged for 45 min at 25,000 rcf (Eppendorf centrifuge, model 5417R). The supernatants were collected and quantitation of EB extravasation was performed as described65 (link). EB levels in each brain were determined from the formula: (A620 nm − ((A500 nm + A740 nm) ∕ 2)) ∕ mg wet weight. One-way ANOVA with Fisher´s LSD (*P < 0.05, **P < 0.01, ***P < 0.001 and ****P < 0.0001) was used.
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4

Blood-Brain Barrier Permeability Assay

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For analysis of BBB permeability, mice were injected with 100 μl of 4% EB dye (Sigma-Aldrich) intravenously. One hour later, animals were perfused with PBS for 4 min and the brains were removed and separated into hemispheres, and each hemisphere was then homogenized in N,N-dimethylformamide (Sigma-Aldrich) and centrifuged for 45 min at 25,000 rcf (Eppendorf centrifuge, model 5417R). The supernatants were collected and quantitation of EB extravasation performed as described [69 (link)]. For experiments with intracerebroventricular injections data from both hemispheres were combined. For experiments following MCAO, the hemispheres ipsilateral and contralateral to the MCAO were analyzed separately and background EB levels in the non-ischemic hemisphere were subtracted from the ischemic hemisphere. EB levels in each hemisphere were determined from the formula: A620nm-A500nm+A740nm/2/mg wet weight.
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5

Cerebral Malaria Brain Vascular Permeability

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At day 6 PI, when C57BL/6J WT mice show signs of CM, the different mouse groups were killed 1 h after retroorbital injection of 100 μL of 2% EB dye (Sigma) and were perfused intracardially with 15 mL of phosphate buffer saline (PBS). Brains were dissected, weighed, and pictured. EB retained in the brain tissue was extracted and measured by spectrophotometry at 620 and 740 nm (Thermo Scientific Multiskan GO Microplate Spectrophotometer). Amounts of EB were calculated using an EB standard and expressed as milligrams of EB per gram of brain tissue.
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6

Evaluating BBB Permeability via Evans Blue

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BBB permeability was determined by measuring Evans blue (EB) extravasation. A solution of 2% EB dye (3mL/kg, Sigma Aldrich, St. Louis, USA) was slowly administered intravenously at 1, 21 and 45 hours after reperfusion onset. Three hours following infusion, animals were perfused with 200 mL saline and decapitated. The brain was dissected into two hemispheres and soaked in methanamide separately for 48 hours. To pellet the brain tissue, the sample was centrifuged for 30 minutes at 14,000 rpm. The absorption of the supernatant was measured at 632 nm with a spectrophotometer (Bio-Rad, Hercules, USA). The EB content was calculated as µg/g of brain tissue using a standardized curve by a blinded observer.
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7

Quantifying Spinal Cord Vascular Permeability

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BSCB integrity was assessed by measuring the extravasation of vascular tracers into the spinal cord parenchyma (Fang et al., 2013b). Briefly, 48 hours after IRI, Evans blue (EB) fluorescence and content were used for the qualitative and quantitative examination of extravasation induced by BSCB disruption after SCIRI, as previously described (Fang et al., 2015). 2% EB dye (10 mL/kg; Sigma-Aldrich, St. Louis, MO, USA) was slowly intravenously administered. The rabbits were anesthetized and perfused with 500 mL/kg saline through the left ventricle after the EB circulated for 1 hour, and the spinal cord (L4–6) was removed. The spinal cord tissue was fixed in 4% paraformaldehyde, sectioned at 10 mm thickness, and frozen and sealed in a dark container before measurement of EB fluorescence. EB staining was visualized using an Eclipse Ci fluorescence microscope (Nikon, Tokyo, Japan). Thereafter, the spinal cord tissue was weighed and soaked in formamide for 24 hours (60°C), and then centrifuged. The absorbance of the supernatant was measured at 632 nm with a microplate reader (Bio Tek, Winooski, VT, USA). The content of EB in the spinal cord tissue was determined (quantified as μg/g) using a standard curve.
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8

Evaluating BBB Permeability with EB Dye

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BBB permeability was evaluated using EB dye as previously described51 (link). On day 21 post-EAE induction, the mice were intravenously injected with EB dye (2% in PBS; 4 mL/kg bodyweight; Sigma), which was allowed to circulate for 1 h. The mice were then perfused with saline (25 mL) and the spinal cord was excised and weighed. The tissues were homogenized in formamide (0.3 mL; Sigma Aldrich) and incubated overnight at 55 °C for EB extraction. The absorbance value of the EB in the extracts was measured at 500 nm. Additionally, the absorbance value was adjusted to the volume of EB using the standard curve prepared using different concentrations of EB. The final value was represented by dividing the volume of EB in the tissue by the tissue weight.
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9

In vivo Evaluation of Blood-Brain Barrier Disruption

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Disruption of blood‐brain barrier (BBB) after photothrombotic stroke was evaluated by in vivo Evans blue (EB) fluorescent imaging.14 Briefly, 2 hours after EB dye (Sigma, 10 mg/mL in saline, 2.5 mL/kg rat weight) was injected via tail vein, animals in each group (n = 6) at day 3 and 7 were killled with an overdose of pentobarbital injection (RMB, Animal Health Ltd., UK). The brains were carefully removed from the skulls immediately after death. To detect the presence of EB, the intact brain was imaged using IVIS 50 (PerkinElmer, UK) with following steps and image acquisition settings: the brains were placed at the center of imaging field, and images were acquired for 2 seconds using Cy5.5 band pass filter channel (excitation/emission wavelength: 615~665 nm/695~770 nm). ROI selection and quantification were performed using living image software 3.2 (IVIS Imaging System, Perkin Elma, UK).
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10

Photothrombotic Stroke BBB Disruption

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Disruption of BBB was evaluated at day 1, 3, 7, and 14 after photothrombotic stroke induction. Briefly, 2 h after EB dye (Sigma, 10 mg/ml in saline, 2.5 ml/kg rat weight) was injected via tail vein, animals were sacrificed with an overdose of pentobarbital injection (RMB, Animal Health Ltd., UK). The brains were then removed from the skulls immediately after death. To detect the presence of EB, the intact brain was imaged using in vivo fluorescence and bioluminescence imaging system (IVIS 50, Perkin Elma, UK) with following steps and image acquisition settings: the brains were placed at the center of imaging field, and images were acquired for 2 s using Cy5.5 band pass filter channel (excitation/emission wavelength: 615~665 nm/695~770 nm). Region of interest (ROI) selection and quantification were performed using living image software 3.2 (IVIS Imaging System, Perkin Elma, UK).
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