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11 protocols using cell culture grade

1

Dexamethasone Effects on hTM Cells

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hTM cells cultured as monolayers in 6-well polystyrene
plates were treated with 100 nM cell culture grade Dex
(Sigma Aldrich) in fresh TMCM when monolayers were
nearly 80% conuflent. Equivolume treatments of ethanol
were used as the vehicle control. Cells were treated with
either Dex or ethanol for 5 days before extracting RNA and
the medium containing Dex or vehicle was changed daily.
hTree replicates consisting of individual sets of treated and
control cells were prepared for each treatment (n = 3).
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2

Genotoxic Damage Evaluation by Micronucleus Assay

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Genotoxic damage was evaluated by a cytokinesis-block micronucleus cytome assay
(Fenech, 2007 (link)). Following the culture
of peripheral blood with the addition of β-cytochalasin, the preparations were
stained with 5% Giemsa stain for microscopic observation. A count of 1,000 cells
per individual was carried out, as suggested by the International Micronucleus
Consortium; considering all binucleated cells with micronuclei, mononuclear,
trinucleated and tetranucleated cells, cells with nucleoplasmic bridges and
bubble protrusions, and those in necrosis and apoptosis. The proliferation index
was calculated for each individual experiment. All reagents used were high
purity or cell culture grade (Sigma-Aldrich Darmstadt, Germany).
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3

MALDI-TOF Mass Spectrometry Reagents

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The following reagents were purchased from Sigma (Gillingham, UK): ≥99.8% ethanol, ≥ 98% (TLC-grade) α-cyano-4-hydroxycinnamic acid (HCCA) matrix, LC–MS grade acetonitrile, cell-culture grade 1.0 N hydrochloric acid (HCl) and 99% ReagentPlus®-grade trifluoroacetic acid (TFA). CHROMASOLVTM LC–MS grade water was purchased from Fluka (Loughborough, UK).
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4

Endothelial Cell Culture Protocol

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EBM-2 Basal Medium and EGM-2 SingleQuot Kit supplement/growth factors were purchased from Lonza Walkersville, Inc. (Walkersville, MD), and EGM Cell Growth Medium-2 was prepared according the manufacturer’s instructions. NRG-1 (ECD, 377-HB) and EGF (236-EG) were purchased from Bio-Techne/R&D Systems. The recombinant human glial growth factor 2 (GGF2; neuregulin-1beta3; USAN - cimaglermin alfa) was provided by Acorda Therapeutics (Ardsley, NY). Calcein AM and 7-AAD were from ThermoFisher Scientific/Molecular probes. AG-1478 and TAK-165 were obtained from Tocris Bioscience (Bristol, UK). AST-1306 was purchased from SelleckChem (Houston, TX). Collagenase II (345 units per mg, CLS-2) was purchased from Worthington biochemical Corporation (Lakewood, NJ), dispase II (04942078001) was from Roche Life Science (Indianapolis, IN) and DNase I was from Sigma (St. Louis, MO). For experiments involving cell stimulation, final concentrations of dimethyl sulfoxide (Cell Culture grade, Sigma) did not exceed 0.1%.
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5

Isolation and Culture of Endothelial Cells

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EBM-2 Basal Medium and EGM-2 SingleQuot Kit supplement/growth factors were purchased from Lonza Walkersville, Inc. (Walkersville, MD), and EGM Cell Growth Medium-2 was prepared according to the manufacturer’s instructions. NRG-1 (ECD, 377-HB) and EGF (236-EG) were purchased from Bio-Techne/R&D Systems. TAK-165 and GI 254023X were obtained from Tocris Bioscience (Bristol, UK) and diluted in dimethyl sulfoxide (Cell Culture grade, Sigma). Collagenase II (345 units per mg, CLS-2) was purchased from Worthington Biochemical Corporation (Lakewood, NJ), dispase II (04942078001) was from Roche Life Science (Indianapolis, IN). D-glucose and DNase I was from Sigma (St. Louis, MO). For experiments involving cell stimulation, final concentrations of dimethyl sulfoxide did not exceed 0.1%.
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6

Fluke Isolation and Culture Protocol

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Fluke infected sheep livers were collected from a local abattoir within 2 h of slaughter and adult fluke isolated from bile ducts. Fluke were washed in pre-warmed PBS (Cell-culture grade, Sigma Aldrich, UK) and then placed individually into 1 mL of sterile Roswell Park Memorial Institute (RPMI) media (Sigma Aldrich) containing 1% penicillin/streptomycin for 2 h to purge caecal contents. Fluke were washed again in PBS and live fluke were placed in groups of 10–15 in 25 cm2 Corning tissue culture flasks (Appleton Woods, UK) in 5 mL RPMI media overnight at 37 °C. Fluke were examined for movement and presence of eggs to confirm viability at the end of the incubation period (∼14 h). Media from flasks containing live fluke was pooled and eggs and debris removed by centrifugation for 20 min at 600 xg at 4 °C. The supernatant was passed through a 0.2 μm filter and frozen at −80 °C in 1 mL aliquots until required. Total protein concentration was measured using the Bradford Assay (Bradford, 1976 (link)).
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7

Mammalian Cell Culture Reagents

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Na2S nonahydrate (99.99% purity), glucose, hydrocortisone, insulin, apo-transferrin, sodium selenite, sodium orthovanadate, uridine (cell culture grade), protease inhibitor cocktail for mammalian tissue extract, puromycin (Sigma P8833), and RIPA buffer were from Sigma. Monobromobimane (FluoroPure grade) was from Molecular Probes. [1-14C]-glucose (56.5 mCi/mmol), [6-14C]-glucose (60.3 mCi/mmol), and [U-14C]-glutamine (281.0 mCi/mmol) were from PerkinElmer. Cell culture media (DMEM with 4.5 g/l glucose, glutamine, and 110 mg/l sodium pyruvate [Cat. # 11995], RPMI 1640 with glutamine [Cat. # 11875], 199 [Cat. # 11150]), fetal bovine serum (FBS) (Cat. # 10437), penicillin/streptomycin mixture (Cat. # 15140), PBS (Cat. # 10010), and DPBS (Cat. # 14040) were from Gibco.
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8

Quantitative Molecular Analysis using RT-PCR

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All reagents were purchased from Thermo-Fisher Scientific except where otherwise noted. All DMSO utilized was cell culture grade (Sigma). RT-PCR data was generated using a CFX Connect Real-Time PCR Detection System (Biorad, Hercules, CA). For assays requiring absorbance and fluorescence measurements, a SpectraMax M2 plate reader was used (Molecular Devices, San Jose, CA).
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9

Evaluating eATP Impact on Immune Response

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To test the effects of eATP on cytokine and immune-related gene expression,
Japanese flounder HKM and PBL cells were treated with 200 or 1000 μM ATP (cell
culture grade, Sigma-Aldrich) for the indicated times, and eATP-induced gene
expression changes in IL-1β, IL-6, IL-11, TNF-α, G-CSF, IFN, Mx, and NF-κ B p65
subunit (p65) were quantified by quantitative real-time PCR (qRT-PCR). For this
aim, one microliter of cDNAs from each source was amplified in a MyiQ™ Two-Color
Real-Time PCR Detection System (Bio-Rad) with corresponding primer pairs (Table 1) in a total
volume of 25 μl using SYBR PrimeScript Ex Taq™ II kit (TaKaRa) under the
following conditions: initial denaturation at 95°C for 30 s, 40 cycles at 95°C
for 5 s, 60°C for 30 s, followed by dissociation curve analysis (55°C to 95°C:
increment 0.5°C for 5 s). β–Actin was used as an internal
reference gene. Agarose gel electrophoresis analyses were performed at the end
of each qRT-PCR to validate specificity of amplification. The identities of all
the qRT-PCR products were further verified by DNA sequencing. The results are
expressed as fold changes in the target gene normalized to the reference gene
and as relative to expression in untreated controls. Data are presented as the
means ± SEM from triplicate experiments.
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10

Multimodal Characterization of Cell Phenotypes

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All reagents were purchased from Thermo-Fisher Scientific except where otherwise noted. All DMSO utilized was cell culture grade (Sigma). Confocal microscopy images were obtained on an Eclipse Ti-E microscope (Nikon, Tokyo, Japan) using a 63X or 20X objective at room temperature. Images were acquired and processed using NIS-Elements and ImageJ. Flow cytometry analysis was performed on a BD LSRFortessa 5 L flow cytometer equipped with FACSDiva (BD Sciences, USA) at the Flow Cytometry Core Facility at the University of Massachusetts Amherst. RT-PCR data was generated using a CFX Connect Real-Time PCR Detection System (Biorad, Hercules, CA). For assays requiring absorbance measurements, a SpectraMax M2 plate reader was used (Molecular Devices, San Jose, CA). Student’s t-test was used to analyze statistical significance between control groups.
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