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61 protocols using pannoramic desk

1

Histological Analysis of Adipose Tissue Transplantation

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Adipose tissues were excised at 1, 2, and 3 months after injection and analyzed by histological staining. The transplanted fat tissues were fixed with 4% polymethylene formaldehyde and embedded with paraffin. Hematoxylin and eosin were used for histological observation of the intrinsic structure of the grafted fat [16 (link)]. Transplanted fat angiogenesis and proliferative cells were observed by CD31+ (1 : 50, Abcam, UK) and Ki67 (1 : 500, Abcam, UK) immunohistochemical staining, respectively. Differentiated fat cells were observed by PPARγ (1 : 250, Abcam, UK) immunofluorescence staining. The immunohistochemical and immunofluorescence assays were performed as reported previously [8 (link)]. Immunohistochemical photomicrographs were obtained under a Pannoramic DESK (3D HISTECH, Hungary) and visualized by Pannoramic scanner, and immunofluorescence photomicrographs were obtained with a Zeiss fluorescence microscope (HLA100, Shanghai, China).
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2

Optimized Immunofluorescence Staining

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To avoid non-specific staining of antibodies from the same species, multiple immunofluorescence staining was performed using the TSA Plus kit based on tyramine signal amplification technics according to the manufacturer’s instructions. Spontaneous fluorescence was removed from paraffin sections using a tissue spontaneous fluorescence quencher immediately after antigen retrieval. All tissue slices were scanned by a Pannoramic Scanner using Pannoramic DESK, P-MIDI, and P250 (3D HISTECH, Hungary). Detailed information on commercial kits and antibodies can be found in the key resources table.
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3

Eosinophil Quantification via Histology

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Histological analysis was performed by staining the eosinophils using the combined eosinophil-mast cell kit (ab150665, Abcam, Cambridge, UK) per the manufacturer’s instructions. The sections were scanned with slide digital scanners Pannoramic DESK (3DHISTECH), and eosinophil infiltration changes were observed using the Pannoramic Viewer (3DHISTECH).
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4

Evaluating Periostin Expression in Mouse Nasal Tissues

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The excised heads of mice were fixed in 10% formalin solution (Sigma-Aldrich) for 1 week and then placed in 0.1 M EDTA buffer (Biosolution Co. Ltd., Seoul, Korea) for 2 weeks to demineralize the skull tissue. After paraffin embedding, nasal tissues were cut into 4-μm thick sections using a microtome. The nasal tissue sections were then deparaffinized and rehydrated, after which immunohistochemical staining was performed using periostin polyclonal antibody (PA5-34641, Thermo Fisher Scientific). The nasal tissue section was incubated with periostin polyclonal antibody diluted 1:100 in antibody diluent (S0809, Dako, Agilent Technologies, Inc., Santa Clara, CA, USA) overnight at 4 °C; after subsequent washing, the tissue was incubated with biotinylated secondary antibody (MP-7801-15, Vector Labs, Burlingame, CA, USA) at room temperature for 30 min. The sections were scanned with slide digital scanners Pannoramic DESK (3DHISTECH, Budapest, Hungary), and periostin level changes were observed using the Pannoramic Viewer (3DHISTECH).
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5

Histological Analysis of Mouse Nasal Mucosa

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After examining the NALF, the mouse heads were removed, fixed in 10% formalin solution (Sigma-Aldrich) for 7 days at 24 °C, decalcified in 0.1 M EDTA buffer (Bio-solution Co. Ltd., Seoul, Korea) for 14 days, and embedded in paraffin. The paraffin-embedded tissue blocks were cut into 5 μm thick sections using a microtome, and the tissues were mounted on slides and stained with hematoxylin and eosin (H&E; Sigma-Aldrich) to analyze the nasal mucosa thickness. A periodic acid Schiff (PAS) staining kit (Sigma-Aldrich) was used to analyze goblet cell hyperplasia, and Giemsa staining solution (Tissue Giemsa stain, BBC Biochemical, Mount Vernon, WA, USA) was used to analyze eosinophil infiltration in the nasal mucosa. Tissue slides were scanned with Pannoramic DESK (3DHISTECH, Budapest, Hungary) digital slide scanners and observed using the Pannoramic CaseViewer software (3DHISTECH).
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6

Immunohistochemical Analysis of Nasal Tissues

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The nasal tissues sections of the mice were deparaffinized in xylene, rehydrated, and washed. For immunohistochemical staining, the nasal tissue sections were incubated overnight at 4 °C with rabbit anti-periostin (1:100 dilution; PA5-34641, Thermo Fisher Scientific), mouse anti-MUC5AC (1:1000 dilution; NBP2-15196, Novus Biologicals, Littleton, CO, USA), and mouse anti-4-hydroxynonenal (4-HNE; 1:100 dilution; bs-6313R, Bioss, Beijing, China) primary antibodies. These antibodies were diluted with antibody diluent solution (cat. no. S0809, Dako, Agilent Technologies, Inc., Santa Clara, CA, USA). Slides were then washed and incubated with secondary antibody (cat. no. MP-7801-15, Vector Labs, Burlingame, CA, USA) for 30 min at 24 °C and then stained with 3,3′-diaminobenzidine (DAB) solution. The slides were scanned with Pannoramic DESK (3DHISTECH) digital slide scanners, and the infiltration of eosinophils and the levels of periostin and MUC5AC were observed using the Pannoramic CaseViewer (3DHISTECH).
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7

Stem Tissue Structure Analysis of Transgenic Poplar

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In order to explore the stem tissue structure of transgenic poplar overexpressing OsCYP85A1 and wild-type plants, fresh petiole segments of each sample were collected and immediately fixed in a formalin–glacial acetic acid–alcohol (FAA) solution containing 3.8% formalin, glacial acetic acid, and 70% alcohol (v:v:v = 1:1:9) for 24 h. During fixing, the air was extracted through a pump. The paraffin sections were prepared according to the method of Miao et al. [30 (link)]. The samples were dehydrated with a series of ethanol solutions and stained with 1% safranine. After they were embedded in paraffin, all cross-sections (20 μm) were cut and stained with 0.1% fast green. The specimens were observed and scanned using Pannoramic DESK (3DHISTECH, Budapest, Hungary). According to the phloroglucinol staining method of Rao et al. [57 (link)], the stems of the seventh section were stained, and the sections were decolorized, observed, and photographed under a NIKON Eclipse Ci (Nikon, Tokyo, Japan).
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8

Quantifying Myocardial Inflammation in Mice

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The hearts of 5 mice in each group were obtained and fixed in 4% paraformaldehyde for 24 h at room temperature. After being paraffin-embedded and sectioned, the sections were stained with hematoxylin and eosin (H&E) and then scanned using Pannoramic DESK (3D HISTECH, Budapest, Hungary). The infiltrated inflammation cells were visualized using the Caseviewer CV2.3 software (3DHISTECH, HUN). The severity of myocardial injury was judged based on the pathological score as described previously [13 (link),28 (link),29 (link),30 (link)]. The myocarditis scoring ranging from 0 to 4 is as follows: 0 indicates no inflammatory infiltrates; 1 indicates small foci of inflammatory cells; 2 indicates larger foci > 100 inflammatory cells; 3 indicates ≤5% of the cross section involved; and 4 indicates >5% of the cross section involved.
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9

Multitissue Histological Analysis of Mice

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After the mice were sacrificed, their heart, liver, spleen, lung, kidney and tumor tissues were embedded and sectioned. Sections were deparaffinized and rehydrated with alcohol-xylene. For HE staining, the sections were then stained with hematoxylin and eosin, scanned using a Pannoramic DESK (3D HISTECH). For Ki-67 and P53 staining, sections were incubated in 3% H2O2 for 25 min to quench endogenous peroxidase activity before they were heated to retrieve the antigen. Then the sections were blocked with 3% BSA for 30 min at room temperature, incubated overnight at 4 °C with antibodies against Ki-67 (27309-1-ap, Proteintech) and P53 (GB13029-3, Servicebio). Histochemical kit (G1430, Servicebio) was used for immunohistochemical analysis. Sections staining were examined using CIC microscope.
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10

Skin Biopsy Sectioning and Laser Microdissection

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Frozen skin biopsy samples were embedded in 10% gelatin (Sigma) and cryosectioned (CM1810, Leica) at 5 μm thickness for histology and 25 μm thickness for laser capture microdissection (LMD7, Leica). Hematoxylin and eosin (H&E) staining was carried out according to the manufacturer’s protocol (Thermo) and the correct orientation was assessed prior to Liquid Chromatography Mass Spectrometry (LCM). The stratum corneum and epidermis, superficial dermis, and deep dermis were dissected from multiple serial sections until 3 million μm2 tissue was obtained from each region of interest, per biopsy sample. Sections were taken either side of sections dedicated to LCM to ensure histological structures of interest did not change throughout the serial sections. Pre- and post-LCM scans were taken from each section dissected using the 5x magnification on the LMD7 scope (Fig. S12). H&E-stained sections were scanned using a Pannoramic Desk digital slide scanner and images were generated in CaseViewer (3DHistech).
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