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24 protocols using paraformaldehyde (pfa)

1

Viral Cytopathic Effect Quantification

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The cells were seeded into a 96-well plate for 24 h. The solution was removed, and monolayers of cells were washed twice with PBS. Then, 10-fold series dilution of viral samples was added to the 96-well plate. Each group was diluted in 8 duplicate wells and cultured at 37°C for 3–5 days. Immunofluorescence assay was conducted to observe and record PEDV-infected cells. Briefly, cells were fixed with 4% paraformaldehyde (Dalian Meilun Biotech Co., Ltd., Dalian) for 15 min and then permeabilized with 0.2% Triton X-100 (Dalian Meilun Biotech Co., Ltd., Dalian) for 10 min at room temperature. After the permeabilization treatment, cells were blocked with 1% bovine serum albumin (BSA) (Beijing Solarbio Science and Technology Co., Ltd., Beijing) and then stained overnight at 4°C with anti-PEDV N polyclonal antibody diluted with 1:10000 (Xu, et al., 2020 (link)). After being washed with PBST three times, cells were incubated with goat anti-mouse secondary antibody (Abcam, Shanghai) diluted with 1:10000 labeled with fluorescein isothiocyanate (FITC) at 37°C for 1 h. The fluorescent particles were observed and counted using a fluorescence microscope (Leica DMi8, Germany).
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2

Histopathological Assessment of Tissue Injury

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The mice were euthanized by CO2 from compressed gas cylinders. Then the tissues were removed and fixed in 4% paraformaldehyde (Meilunbio, China) for more than 24 h, and embedded in paraffin. The sections (thickness, 6 μm) were stained with hematoxylin & eosin or Periodic acid-Schiff (PAS) solutions (Servicebio, China). The tissues injury scores and the number of PAS-positive cells per unit of length (mm) of the basement membrane were determined in 5 randomly selected nonoverlapping fields from respective individual tissue sections using a microscope (DMi8; Leica) and all histology analyses for H&E staining were conducted in a blinded manner as a combination of tissue damage (score 0–5) and inflammatory cell infiltration (score 0–5) with a total ranging from 0 to 10. The number of PAS-positive cells per unit of length (mm) of the basement membrane were assessed with ImageJ software version 1.52 (National Institutes of Health software, Maryland, USA).
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3

Clonogenic Assay for Cell Proliferation

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Logarithmically growing cells of interest were collected and seeded into 6-well plates (500 cells per well) and cultured in an incubator for 14 days. After the incubator culture was completed, the original medium was discarded. The 4% paraformaldehyde (Meilunbio, China), 0.1% crystal violet staining solution (Meilunbio, China) and PBS were used to fix, stain, and wash. Subsequently, the 6-well plate was placed in a fume hood to dry. Colonies larger than 50 cells were counted. Three independent experiments were performed in each experimental group.
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4

Measuring HCC Cell Migration and Invasion

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Hep3b and Huh7 cells were added into the upper chambers of Matrigel-uncoated (cell migration) or coated (cell invasion) Transwells (ET BIOFIL, Guangzhou, TCS004024). The lower chambers were added medium with 10% FBS, and the upper chambers were serum-free medium. After 24 h culture, the migrated or invaded cells (on the bottom of the filters) were fixed using 4% paraformaldehyde (Mei Lun, China, MA0192) and stained with 0.5% crystal violet for 1 h. The number of migrated or invaded HCCs was counted under a light microscope by randomly selecting five fields.
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5

Colony Formation Assay Protocol

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Cells were inoculated in a six-well plate at a density of 1,000 cells per well and cultured in an incubator for 2 weeks. The medium was discarded, and every well of the culture plate was gently rinsed twice with PBS and fastened with 4% paraformaldehyde (Meilunbio, Dalian, China) for 20 min and stained with 0.5% crystal violet (Solarbio, Beijing, China) for 20 min. After staining was completed, the colonies were scanned and imaged by 3D HISTECH scanner (Budapest, Hungary).
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6

Transwell-based Metastasis Assay for Prostate Cancer

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Transwell chambers (Corning, United States) were used to assess prostate cancer cell metastasis ability. The upper inserts of 24-well Transwell chambers were added, and 2 × 104 cells were resuspended in 0.1 ml of serum-free medium. Then, 0.6 ml of medium with 30% FBS was added to the lower compartments as a chemoattractant. After 24 h of culture, the cells on the surface of the membrane were gently removed with cotton buds, fixed with 4% paraformaldehyde (Dalian Meilun Biotechnology, Dalian, CN) for 15 min, washed three times with PBS, fixed and stained with 0.1% crystal violet for 30 min. The stained cells were photographed under an inverted fluorescence microscope (magnification ×200; Olympus, TKY, JPN). Five visual fields were observed in each group.
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7

Evaluating EZH2 and AURKA Inhibitors

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Hep3B and Huh7 cells (a total of 5×106) were plated into 6-well plates, respectively. After treatment with an EZH2 inhibitor (2 μM gambogenic) or an AURKA inhibitor (10 μM alisertib) for 72 h, colonies were fixed with 4% paraformaldehyde (Mei Lun, China, MA0192) and stained with crystal violet (Beyotime, Shanghai, C0121-100 ML) for 30 min at room temperature. The visible colonies were counted manually. All assays were conducted at least three times.
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8

Evaluating EZH2 and AURKA Inhibitors

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Hep3B and Huh7 cells (a total of 5×106) were plated into 6-well plates, respectively. After treatment with an EZH2 inhibitor (2 μM gambogenic) or an AURKA inhibitor (10 μM alisertib) for 72 h, colonies were fixed with 4% paraformaldehyde (Mei Lun, China, MA0192) and stained with crystal violet (Beyotime, Shanghai, C0121-100 ML) for 30 min at room temperature. The visible colonies were counted manually. All assays were conducted at least three times.
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9

Histological Analysis of Dentine Formation

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Samples were fixed in 4% paraformaldehyde for 24 h and decalcified in 10% EDTA (pH 7.4, MeilunBio, China) for 3 months, and then, all samples were embedded in paraffin and cut into 5 μm sections. For histological analysis, sections were stained with H&E solution. Next, we counted the number of odontoblasts and measured the thickness of the new dentine using ImageJ software (1.50i, National Institutes of Health, Bethesda, MD, USA).
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10

MicroRNA Mimics for Cell Studies

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The microRNA-21 mimic (miR-21),
microRNA-155 mimic (miR-155), and 6-carboxy-fluorescein (FAM)-labeled
microRNAs were synthesized by GenePharma (Shanghai, China). The sense
strand sequence of miR-155 was 5′-UUAAUGCUAAUCGUGAUAGGGGUU-3′.
The sense strand sequence of miR-21 was 5′-UAGCUUAUCAGACUGAUGUUGA-3′.
All of the chemical reagents used in this paper were purchased from
Sigma-Aldrich unless otherwise noted, and all reagents were analytical
grade. Methoxy poly(ethylene glycol)-acrylamide (mPEG-AC, Mw 2000)
was purchased from Huateng Pharma (Hunan, China). Culture medium,
paraformaldehyde, and CCK-8 kit were supplied by Dalian Meilun Biotechnology
Co., Ltd. (Dalian, China). 4′,6-Diamidino-2-phenylindole (DAPI)
was purchased from Beyotime Biotechnology Co., Ltd. (Shanghai, China).
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