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16 protocols using warp red

1

Quantitative Immunohistochemistry of Macrophages, Mast Cells, and Vessels in Adipose Tissue

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Part of each biopsy was fixed in phosphate-buffered formalin, processed (Leica TP 1020, Leica Microsystems), embedded in paraffin, and cut into 5-μm-thick sections. The sections were subjected to high-temperature antigen retrieval for 10 min in EDTA buffer, pH 8, followed by blocking and incubation with antibodies against macrophages (Monoclonal mouse anti-human CD68, clone PG-M1, M0876, Dako, Glostrup, Denmark), mast cells (monoclonal mouse anti-human mast cell tryptase, clone AA1, M7052, Dako), and von Willebrand factor (polyclonal rabbit anti-human von Willebrand Factor, A0082, Dako) to detect vessels. For visualization of immunoreactions, MACH3 mouse AP-polymer (M3M532) was used for macrophages and mast cells and MACH3 Rabbit AP-Polymer (M3R533) for vessels (Biocare Medical, Concord, CA). The chromogen was Warp Red (WR806, Biocare Medical). Slides were counterstained with hematoxylin, mounted, scanned with a Mirax Digital Desk Scanner (Zeiss, Göttingen, Germany), and analyzed with Tissue Studio 3.6.1 (Definiens, Munich, Germany). Macrophage and mast cell densities were expressed as the number of immunoreactive cells per 103 adipocytes. Vessel density was expressed as positive signal area per adipocyte.
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2

Quantifying Adipose Tissue Macrophages

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Paired subcutaneous and visceral adipose tissue specimens were fixed in phosphate-buffered formalin, dehydrated, embedded in paraffin and sectioned at 4 μm. After hydration and heat-induced antigen retrieval, a monoclonal antibody targeted at human CD68 was added to detect macrophages (Anti-Human CD68 clone PG-M1, DakoCytomation, Denmark). MACH 3 Mouse AP-Polymer and Warp Red was used as secondary and detection reagents (Biocare Medical Concord, CA). The sections were counter stained with hematoxylin and mounted. Slides were digitalized (Mirax Desk Digital Slide Scanner, Zeiss, Göttingen, Germany) and macrophages were counted and normalized for analyzed section area (Mirax Viewer, Zeiss). Origin of the tissue was unknown to the observer.
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3

Immunohistochemical Analysis of COX2 in FFPE Tissues

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Four µm sections of FFPE tissue were stained for single or dual COX2 IHC, or dual COX2 IF. Positive control breast cancer tissue has been previously described31 (link). Detailed protocols for staining are outlined in Supplementary Table 4. COX2 antibody clones were SP21 (Thermo Fisher scientific #RM-9121), CX229 (Cayman #160112), and CX294 (Agilent Dako #M3617). Secondary antibodies and chromogens were Envision+ HRP detection (Agilent #K4001 and #K4003) followed by 3,3′-diaminobenzidine (Agilent #K3468), or alkaline phosphatase detection (Enzo Life Sciences #ACC110-0150) followed by Warp Red (Biocare #WR806) for IHC staining and Alexa Fluor antibodies (Invitrogen #A11029 and #A21245) for IF staining. IHC and IF stained slides were scanned using Aperio ScanScope AT (Leica Biosystems, Vista, CA) and Apotome (Zeiss, Jena, Germany) microscopes, respectively. IHC signal data were captured and quantified using Aperio ImageScope analysis software (Leica Biosystems, Vista, CA)31 (link). All data acquisition was performed by investigators who were blinded to study group.
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4

Histopathological and Immunohistochemical Analysis of Tissues

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As previously described, representative liver, kidney, heart, brain, stomach, spleen, lung, uterus, urinary bladder, cecum, and small and large intestine samples were collected during necropsy and fixed in 10% buffered formalin for 24 h [18 (link)]. The tissues were subsequently transferred to 70% ethanol prior to being processed and embedded. Sections were stained with hematoxylin and eosin for histopathological evaluation. For immunohistochemistry (IHC), 3–4 μm sections were deparaffinized in CitriSolve (Decon Labs., King of Prussia, PA, USA) and rehydrated by processing through graded alcohols. Tissues were pretreated with Proteinase K (10 μg/mL) for 15 min. Endogenous IgG and non-specific background were blocked with Rodent Block M (Biocare Medical; Pacheco, CA, USA) for 20 min, followed by an alkaline phosphatase block (BLOXALL; Vector Laboratories, Burlingame, CA, USA) for 10 min. The primary antibody (PA1-7206; Thermo Fisher Scientific, Waltham, MA, USA) was incubated on the tissue sections at a dilution of 1:10,000 for 1 h at room temperature. Sections were sequentially incubated with a rabbit-on-rodent tissue alkaline phosphatase-based polymer and Warp Red (Biocare Medical, Pacheco, CA, USA). Tissues were counterstained with Tacha’s hematoxylin and mounted using EcoMount (Biocare Medical, Pacheco, CA, USA) [18 (link)].
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5

Immunohistochemical Profiling of NBCe1 in Tissue Samples

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The tissue microarrays were heated and subjected to deparaffinization in xylene, rehydration in graded series of ethanol, and rinsing with distilled water. The slides were then heat treated with the target retrieval solution DIVA Decloaker (Biocare Medical) using an electric pressure cooker for 20 min. After washing, the slides were blocked with Background Sniper (Biocare Medical) at room temperature for 10 min, washed and incubated with anti-NBCe1/SLC4A4 antibody (product no. HPA035628; Millipore Sigma; Merck KGaA) diluted at 1:200 at 4°C overnight. The slides were washed and then incubated with MACH 2 Rabbit AP-Polymer (cat. no. RALP525; Biocare Medical) for 30 min at room temperature. The slides were stained with the chromogen solution Warp Red (BioCare Medical) at room temperature for 7 min. Nuclei were counterstained with hematoxylin at room temperature for 45 sec. Digital images of stained slides were captured using a Biotek Lionheart FX microscope. The images were then evaluated by a histopathologist.
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6

Immunohistochemical Staining for Protein Kinase

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Tissue sections, 3–4 μm in thickness, were deparaffinized in CitriSolve (Decon Labs., King of Prussia, PA) and rehydrated by processing them through graded alcohol solutions. Antigen unmasking was accomplished by digesting tissue in 10 μg/ml of protein kinase for 15 min at room temperature (Fisher Scientific, Waltham, MA). Endogenous enzymes and non-specific background were blocked with Background Punisher (Biocare Medical, Pacheco, CA), followed by BLOXALL (Vector Laboratories, Burlingame, CA). The primary antibody (NBP1–42140; Novus Biologicals, Centennial, CO) was incubated on the tissue sections at a dilution of 1:100 for 1 h at room temperature. Subsequently, sections were sequentially incubated with an alkaline phosphatase-based detection polymer kit (MACH 4; Biocare Medical), and Warp Red (Biocare Medical). Sections were counterstained with Tacha’s hematoxylin (Biocare Medical) and mounted using a permanent mounting medium (EcoMount; Biocare Medical).
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7

Optimized IHC Staining Protocol

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Formalin-fixed, paraffin-embedded tissues were cut at 5 μm thickness. We used the BenchMark XT automated slide staining system (Ventana Medical Systems Inc.) to optimize antibody dilutions and staining. The antigen retrieval step (basic pH tris base buffer) was performed using the Ventana CC1 solution. Primary antibody incubation of sections was for 1 hour. The Ventana iView DAB detection kit was used as the chromogen, and the slides were counterstained with hematoxylin.
For double-IHC staining, the BenchMark XT automated slide staining system (Ventana Medical Systems Inc.) was used for deparaffinization and antigen retrieval. The antigen retrieval step was performed using the Ventana CC1 solution, which is a basic pH tris base buffer. Tissue was incubated with the antibody cocktail for 1 hour at 37°C. Tissue was then incubated with mouse AP (alkaline phosphatase) + rabbit horseradish peroxidase (HRP) polymer detection kit (Biocare Mach 2 Double stain 1) for 30 min at RT. Tissues were rinsed with tris-buffered saline and incubated with chromogens Betazoid DAB and Warp Red (both Biocare) for 5 min each, respectively. Slides were counterstained with hematoxylin, dehydrated, cleared, and coverslipped. The Aperio VERSA 8 slide scanning system from Leica Biosystems, equipped with a Point Grey Grasshopper3 color camera for bright-field scanning, was used to analyze stained sections.
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8

ZIKV Infection Induces Histopathological Changes

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ZIKV-infected RM sacrificed on day 3 and day 14-15 p.i. were subjected to histopathologic analyses. For histopathologic examination, various tissue samples were fixed in 10% neutral buffered formalin, paraffin-embedded, sectioned at 5 μm, and stained with hematoxylin and eosin (H&E). To define specific cell types, we performed immunohistochemistry (IHC) analysis by using antibodies against glial fibrillary acidic protein (GFAP, Agilent Technologies, M0761), and Caspase-3 (Cell Signaling, 9662). IHC staining on sections of brain from both ZIKV-infected and uninfected animals was performed using a biotin-free polymer system (Biocare Medical). The paraffin-embedded sections were subjected to deparaffinization in xylene, rehydration in graded series of ethanol, and rinsed with double distilled water. The brain sections were incubated with rabbit anti-human GFAP and Caspase-3 antibodies for 1h after heat-induced epitope retrieval. Antibody labelling was visualized by development of the chromogen (Warp Red or DAB Chromogen Kits; Biocare Medical). Digital images of brain were captured at 100x and 200x magnification with an Olympus BX43 microscope equipped with a digital camera (DP26, Olympus) and evaluated using Cellsens digital imaging software 1.15 (Olympus).
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9

Immunohistochemical Analysis of Pancreatic Islet Cells

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FFPE pancreas serial cross-sections (4 μm thick) were deparaffinized and rehydrated. Heat-induced epitope retrieval was performed using Borg Decloaker (Biocare Medical, Pacheco, CA) according to the manufacturer's instructions prior to staining with 2 antibody panels: (i) rabbit anti-Ki67 (clone EPR3610, diluted 1:1000, RRID: AB_10562976; Abcam, Waltham, MA, USA), rabbit anti-insulin (clone EPR17359, diluted 1:2000, RRID: AB_2716761; Abcam), mouse anti-glucagon (clone K79bB10, diluted 1:1,000, RRID: AB_297642; Abcam) (Fig. 1A); and (ii) rabbit anti-somatostatin (polyclonal, diluted 1:1,000, RRID: AB_2688022; Agilent Technologies, Inc., Santa Clara, CA, USA), rabbit anti-insulin (clone EPR17359, diluted 1:2,000, RRID: AB_2716761; Abcam), and mouse-pancreatic polypeptide (clone MM0858-31R25, diluted 1:750, RRID:AB_2904511; Abcam) (Fig. 1B). Chromogen-based immunohistochemistry (IHC) staining was detected using a Mach2 Double Stain1/Mach2 Double Stain 2 HRP-AP Polymer Detection Kit according to the manufacturer's instructions (Biocare Medical, Pacheco, CA) with Betazoid DAB (Ki67 or somatostatin), Warp Red (insulin), and Ferangi Blue (glucagon or pancreatic polypeptide; all from Biocare Medical). Slides were counterstained with hematoxylin.
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10

Histopathological Examination of Viral Lung Infection

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Histopathology and detection of viral NP in the lung (immunohistochemistry) were performed at the Yerkes National Primate Research Center (Emory University, GA) according to procedures published previously (37 (link)). Briefly, the whole lungs were collected immediately after euthanization, fixed by submerging the tissues in 10% neutral buffered formalin, and embedded in paraffin. Five-micrometer sections of each lung lobe were taken and stained with hematoxylin and eosin (H&E). For immunohistochemistry staining, lung sections were stained with multisubtype mouse anti-NP antibody (1:1,000 dilution; MAB8251; Millipore, CA) by incubating them at room temperature for 1 h. The labeled tissue sections were stained with Mouse Mach2 (Biocare Medical), and all reactions were detected by development of the chromogen (Warp Red; Biocare Medical). Appropriate positive and negative controls were run in parallel. The nuclei were then counterstained using Gill's hematoxylin. Pathological scores were determined as described previously (38 (link)). Percent lung affected, severity of alveolitis and bronchiolitis/bronchitis, and extent of peribronchial and peribronchiolar/perivascular infiltrates were given the following scores: 0, no lesions; 1, ≤25%; 2, 25 to 50%; 3, >50%. Alveolar edema, hemorrhage, and type 2 pneumocyte hyperplasia were scored 0 if not present or 1 if present.
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