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12 protocols using clearmount

1

In Situ Detection of SARS-CoV-2 RNA

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SARS CoV2 RNA was visualized by RNAscope in situ hybridization with anti-sense probes and reagents from Advanced Cell Diagnostics as previously published (Deleage et al., 2016 (link)). Briefly, slides were boiled in RNAscope Pretreat citrate buffer for 15 minutes. Pretreat reagent 3 (protease solution) was added at a 1:15 dilution, and the slides were incubated for 20 minutes at 40°C in the hybridization oven. SARS-CoV-2 antisense probes VnCoV2019S 21631–23303 of NC 045512.2, which hybridizes specifically to the 5’ end of SARS-CoV-2-Spike RNA, and VnCoV-N 28275–29204 of MN908947.3, which cross-hybridizes to SAR-CoV and MERS N-RNA, were added for 2 hours before continuing with AMPs 1–6 from the RNAscope 2.5 Red detection kit. Warp red chromogen was added to visualize the RNA for 5 minutes. Some sections were then blocked with Peroxidizer 1 and Background Sniper before adding CD68 (diluted 1:300, Dako) overnight. Polink-2 Plus HRP Mouse (GBI Labs) was added according to the manufacturer’s directions. ImmPact DAB was added to visualize macrophages before counterstaining all slides with CAT Hematoxylin and bluing in TBST. A thin layer of Clear mount diluted 1:5 in DI water (Thermo Scientific) was added to the sections, allowed to dry, dipped in xylenes before mounting in Permount.
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2

Trophoblast Invasion Assay for Decidualization

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This assay was performed using 24-well transwell plates (0.8 μm) (Corning #3422) as follows. Briefly, THESCs were plated in the lower chambers and either left undecidualized or decidualized (with and without CB treatments) for 7 days. The cells were then maintained for 24 h in normal OPTI-MEM devoid of MPA, E2 and FK as well as CB to allow accumulation of secretory factors from decidualized THESCs. On day 8, Martigel (0.2 mg/ml) (Invitrogen #354263) coated transwells were inserted and seeded with 1 × 105 of HTR8-SV/neo (HTR8) cells suspended in serum-free F12-K. After 24 h of incubation, the transwells were placed in 4% ice-cold formaldehyde for 5 minutes to fix the cells. Cotton buds were used to gently clear the martigel. Invading HTR8 trophoblast cells were stained with crystal violet (0.5% w/v in methanol) for one minute and repeatedly washed in PBS to remove excess staining. Individual membranes were gently cut and mounted on positively charged glass slides using ClearMount (ThermoFisher #00–8110). The numbers of invading HTR8 cells in each treatment group were counted and graphed from four random images from inverted microscope (Nikon Eclipse Ti).
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3

Immunofluorescence Visualization of Epithelial-Mesenchymal Transition

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Cultured NCI-H322M cells grown on coverslips in a 24-well plate were fixed with 2% paraformaldehyde (Nacalai Tesque, Kyoto, Japan) for 30 min, washed with PBS, and permeabilized with 0.1% Triton-X-100 (Thermo Fisher Scientific) in PBS for 15 min. Following a PBS wash, non-specific proteins were blocked with 2% BSA (Fujifilm Wako Pure Chemical) for 15 min. The cells were incubated with a mixture of two primary antibodies: anti-E-cadherin rabbit monoclonal antibody (1:200 dilution, 24E10; Cell Signaling Technology) and anti-N-cadherin mouse monoclonal antibody (1:200 dilution, 610920; BD Biosciences) for 1 h at RT. Coverslips were washed with PBS and incubated with CF®488A goat anti-rabbit IgG (1:200 dilution, Biotium, Hayward, CA, USA) and CF®568 goat anti-mouse IgG (1:200 dilution, Biotium) antibodies in the dark for 15 min. Following a PBS wash, nuclei were stained with Hoechst 33342 (5 μg/mL; Nacalai Tesque) for 15 min. The cells were then washed and mounted in an aqueous-based mounting medium, ClearMount™ (Thermo Fisher Scientific). Images were captured with a 60 × oil objective lens on an Olympus Fluoview FV10i confocal microscope (Olympus, Tokyo, Japan).
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4

Immunohistochemical Analysis of Collagen Types

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To perform immunohistochemistry of type II collagen (1:1, Iowa Hybridoma
Bank, Iowa), type VI collagen (1:200, Fitzgerald, Cambridge UK), or type I
collagen (1:800, Abcam, Cambridge MA), sections were treated with xylenes and a
decreasing ethanol series, incubated for 5 min with Digest-All 3 pepsin
digestion (Thermo Fisher), treated with 30% peroxidase, blocked with goat serum,
incubated with primary antibody for 1 h at room temperature, incubated with
secondary antibody (ab97021 for type II and type I collagen, ab6720 for type VI
collagen, Abcam, 1:500) for 30 minutes, treated with HRP streptavidin and AEC
Red Single (Histostain-Plus BS, Thermo Fisher), counterstained with hematoxylin,
and mounted with Clearmount (Thermo Fisher). Human osteochondral sections were
used as both positive and negative controls.
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5

Immunohistochemistry Protocol for IHC

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For IHC 75 (link), 5 µm tissue sections were cut, mounted, dewaxed and rehydrated and then treated as described in Table S4. Epitope retrieval (15 min at 98–100°C) was followed by blocking (TBS+0.5% casein; 10 min), rinsing [TBS+0.05% Tween-20 (TBS-Tw)] and an incubation with primary antibody (60 min). Samples were washed in TBS-Tw and blocked using 1.5% H2O2 in TBS-Tw (5 min) (peroxidase block was not performed for MPO-IHC). Horseradish peroxidase-conjugated secondary antibodies (Table S4) were detected using ImmPact-DAB substrate (Vector Labs). All slides were washed in distilled water, counterstained with hematoxylin, mounted with Clear Mount (Invitrogen), dried for 60 min at 40°C and mounted with Permount (Electron Microscopy Sciences).
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6

Immunohistochemistry Protocol for IHC

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For IHC 75 (link), 5 µm tissue sections were cut, mounted, dewaxed and rehydrated and then treated as described in Table S4. Epitope retrieval (15 min at 98–100°C) was followed by blocking (TBS+0.5% casein; 10 min), rinsing [TBS+0.05% Tween-20 (TBS-Tw)] and an incubation with primary antibody (60 min). Samples were washed in TBS-Tw and blocked using 1.5% H2O2 in TBS-Tw (5 min) (peroxidase block was not performed for MPO-IHC). Horseradish peroxidase-conjugated secondary antibodies (Table S4) were detected using ImmPact-DAB substrate (Vector Labs). All slides were washed in distilled water, counterstained with hematoxylin, mounted with Clear Mount (Invitrogen), dried for 60 min at 40°C and mounted with Permount (Electron Microscopy Sciences).
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7

Fluorescent Nanodroplet Uptake in Breast Cancer Cells

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Fluorescent microscopy uptake studies were conducted using FITC-labeled, AS1411-conjugated nanodroplets. Images were acquired using an EVOS FL digital fluorescence microscope (Advanced Microscopy Group, Mill Creek, WA, USA). Human MDA-MB-231 breast cancer cells were plated for 48 hr at a density of 4,000 cells/cm2 in glass cell culture dishes (FluoroDish, World Precision Instruments, Sarasota, FL USA). AS1411-conjugated fluorescent nanodroplet emulsions were added to cells at various doses (4%, 2%, 1%, 0.4%, 0.2% and 0% v/v PFP) and incubated for various amounts of time (0, 1, 4, 24, 48, and 72 hr) at 0.4% v/v PFP. Slides were washed with HBSS, fixed with 3.5% paraformaldehyde, stained with 0.05% Hoechst 33342 for 5 minutes at room temperature to detect nuclei, washed twice, and mounted (ClearMount, Invitrogen, Frederick, MD, USA) for at least 3 hours prior to imaging. All images were acquired with identical microscope settings (60% brightness for FITC and 10% brightness for Hoechst). Fluorescence intensity of FITC in cells was quantified using ImageJ.
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8

Immunohistochemistry of Bladder Tissue

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Isolated whole bladders were pre-fixed in 4% paraformaldehyde overnight and cryoprotected in 30% sucrose. The samples were embedded in OCT compound (Leica Microsystems, Germany), cryosectioned into 10 m thick slices, and mounted on microscope slides. After permeabilization in a solution containing 0.5% triton X-100 and 6% bovine serum albumin for 1 hour, the sections were incubated overnight at 4 °C with primary antibody [Anti- -smooth muscle actin (#ab21027, Abcam), 1:200]. The sections were then washed three times with 1X PBS and incubated with the secondary antibody [Alexa Fluor 594 Donkey Anti-Rabbit IgG (#A21207, Invitrogen), 1:1000] for 1 hour at room temperature. The sections were subsequently washed three times with PBS and stained with DAPI (#R37606, Molecular Probes) to visualize the nuclei. Finally, the sections were rinsed with PBS three times and mounted with Clearmount (#008010, Invitrogen, UK). Confocal fluorescence images were acquired using a ZEISS scanning laser microscope with a 20X or 40X oil immersion objective lens (CLSM780, ZEISS, Germany).
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9

Immunofluorescence Labeling of Epithelial-Mesenchymal Markers

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Cultured cells grown on coverslips in a 24-well plate were fixed with 2% paraformaldehyde (Sigma-Aldrich) for 30 min, washed in PBS, and then permeabilized with 0.1% Triton-X-100 (Fisher Scientific, Pittsburgh, PA) made in PBS for 15 min. Following a PBS wash, non-specific proteins were blocked in 2% BSA for 15 min at RT. The cells were incubated with a mixture of two primary antibodies: monoclonal rabbit antibody to vimentin (1:100, ab92547, Abcam) and monoclonal mouse antibody to E-cadherin (1:50, ab1416, Abcam) in a humidified atmosphere for 1 hour at 37°C. Coverslips were then probed with Alexa Fluor 488 goat anti-mouse IgG and Alexa Fluor 555 goat anti-rabbit IgG (both; 1:200, Abcam) in the dark for 15 min at RT. Following a PBS wash, nuclei were stained with Hoechst 33342 (50 μg/ml) for 5 min at RT, washed and mounted in an aqueous-based mounting medium Clearmount™ (Invitrogen). Images were captured with the 40X oil objective lens on the Olympus Provis fluorescence microscope (Olympus Optical).
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10

Insulin-positive Cells Morphometric Analysis

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5 μm-thick deparaffinized sections were subjected to heat induced epitope retrieval procedure (HIER) in a citrate buffer (Dako) using a microwave. To eliminate endogenous peroxidase activity, the sections were pretreated at room temperature with 3% H2O2 in methanol for 10 minutes. Sections were then incubated with the primary antibody against insulin (Santa Cruz, sc-9168) diluted 1:100 in 1× PBS overnight at +4°C in a moist chamber [26 (link)]. The reaction was detected using Histostain SP kit (Invitrogen) while staining was visualized using AEC chromogen. Slides were counterstained in hematoxylin and mounted using ClearMount (Invitrogen). Each slide was analyzed by microscope (Olympus Provis, Campbell) and photographed (magnification 40×) covering its entire surface. For the determination of beta islet size, number and diameter pancreatic sections stained for insulin and hematoxylin were analyzed. An islet was defined as a cluster of four or more insulin-positive cells. After careful assessment of the entire pancreatic section, five representative islets from five different microscopic fields from five paraffin blocks randomly selected from each group (5 rats from each group) were identified and islet size and diameter were measured. The computed morphometric image analysis and measurements of the digitalized images were carried out using Sform software (Vams).
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