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9 protocols using anti nfat1

1

Immunofluorescence Staining of Monocytes

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Monocytes or their sorted subsets were seeded into μ‐Slide VI 0.4 (IBIDI) at a concentration of 0.7–1 × 106/ml and incubated for 1 h (37°C, 5% CO2). Cells were washed in PBS and fixed with 4% formaldehyde for 15 min at 4°C. BSA (2.5%, Santa Cruz Biotechnology, Dallas, TX, USA) was used for blocking. Samples were incubated overnight with anti‐PTX‐3 (ab90806, Abcam, Cambridge, UK), anti‐CD14 biotinylated (eBiosciences) and anti‐NFAT1 (Cell Signaling Technologies) antibodies. For detection, secondary antibodies AF488 Donkey anti‐rabbit and AF555 Goat anti‐rat (Thermo Fisher Scientific) and streptavidin AF‐647 (eBiosciences, Thermo Fisher Scientific) were used. All antibodies were diluted in DAKO Antibody diluent (DAKO). DAPI (Sigma Aldrich) was used as a nuclear counterstain. Samples were mounted in Mowiol 40–88 (Sigma Aldrich) and images were captured under a Zeiss LSM 780 confocal microscope fitted with a 40 (1.3 numeric aperture) oil‐immersion objective. Image processing was performed in FIJI.33
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2

Immunohistochemical Quantification of ASIC2 and NFAT1

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Following deparaffinization and rehydration, tumor sections (3-μm thickness) were incubated in 0.3% H2O2 in methanol for 30 min at 37 °C to block endogenous peroxidase. The sections were then boiled in 10 mmol/L citrate buffer (pH 6.0) for 2 min in an autoclave. The anti-ASIC2 (Abcam) or anti-NFAT1 (Cell Signaling) antibody was added and the sections were incubated at 4 °C overnight. The sections were visualized by using the diaminobenzidine solution (DAKO, Carpinteria, CA, USA), and then lightly counterstained with hematoxylin. Sections without incubation with primary antibody served as negative controls. The intensity of staining (brown color) was semi-quantitatively scored as follows: 1, weak; 2, medium; 3, strong; and 4, very strong. The percentage of maximally stained tumor cells in each section was recorded (0, <5%; 1, 5–30%; 2, 30–50%; 3, >50%). High expression of ASIC2 was defined as a combined score for the intensity and area of staining that was larger than 4. The results were verified by two pathologists independently.
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3

NFAT-mediated Cxcr5 Regulation in T Cells

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Nuclear extracts from murine Tconv and Foxp3+ Treg cells as well as whole cellular extracts from transiently transfected HEK 293T cells were prepared using the ProteoJET kit (Thermo Fisher Scientific). EMSA was performed, as previously described (Schmidt et al., 2008 (link)), with the following probes: Cxcr5-N1, 5′-GAAAAGACTCAGTGGAAAAAAAAAAAAAAAG-3′; Cxcr5-N1mut, 5′-GAAAAGACTCAGTAAAAAAAAAAAAAAAAAG-3′; Cxcr5-N2, 5′-GGGGGGAGTTTCCCTTTTTCTTAAA-3′; Cxcr5-N3, 5′-GGGATGGTTGGTCACCCTAGTGATAAGGAAAGTG-3′; Cxcr5-N4, 5′-GGACTGAGGGGTTTCCCAGGACAGGGGACTT-3′; IL2-Pubd, 5′-CCCCAAAGAGGAAAATTTGTTT-3′. The mutations are underlined. For super-shifting anti-NFAT2 (7A6; BD) and anti-NFAT1 (Cell Signaling Technology) Abs were used.
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4

Visualization of NFAT1 nuclear translocation

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THP‐1 cells were maintained in RPMI 1640 with 10% FBS (Sigma Aldrich) and peripheral blood monocytes were cultured in X‐VIVO 15 (Lonza) without any supplementation at 37°C in 5% CO2 atmosphere. The cells were seeded at 1 × 106/ml into the plate (THP‐1) or μ‐Slide VI 0.4 (IBIDI; primary monocytes) and stimulated with ionomycin (1 μg/ml, Sigma Aldrich) for 30–90 min in the presence or absence of CsA (1 μg/ml, Cell Signaling Technologies). THP‐1 cells were then harvested and spun to generate a cytospin preparation, which were fixed by incubation in 4% formaldehyde for 15 min at 4°C. Primary monocytes were fixed in 4% formaldehyde immediately in a μ‐Slide VI 0.4 chamber. BSA (2.5%, Santa Cruz Biotechnology) was used for blocking. Samples were incubated overnight at 4°C with anti‐NFAT1 (#4389, Cell Signaling Technologies) and biotinylated anti‐CD14 (eBiosciences) antibodies that were subsequently detected using AF488 donkey anti‐goat (Thermo Fisher Scientific) and AF647 streptavidin (eBiosciences) secondary antibodies. All antibodies were diluted in DAKO Antibody diluent (DAKO). DAPI (Sigma Aldrich) was used as a nuclear counterstain. Samples were mounted in Mowiol 40–88 (Sigma Aldrich). Images were acquired using a Zeiss LSM 780 confocal microscope with ×40 (1.3 numeric aperture) oil‐immersion objective. Image processing was done using FIJI.33
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5

Quantification of NFAT1 Activation

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Total protein extracts were isolated with M-PER protein extraction kit (Thermo Scientific) and quantified with a BCA kit (Thermo Scientific). 20µg of protein extract were loaded per lane, separated on a 10% SDS-PAGE gel and transferred to a nitrocellulose membrane. anti-NFAT1 and anti-β-actin were obtained from Cell Signaling Technology. Anti-pNFAT (Ser213/217/229) antibody was obtained from Santa Cruz Biotechnology (Dallas, TX). Primary antibodies were detected by secondary anti-rabbit-HRP-conjugated (Cell Signaling Technology) and images were obtained in a CCD camera instrument. Bands were quantified with QuantityOne software.
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6

NFAT1 Expression in Activated NK Cells

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PBMCs from HD were stimulated for 1 hr with ionomycin at the indicated concentration. They were then stained with a fixable viability dye (ThermoFisher Scientific) and stained for surface markers allowing NK cell identification (CD3, CD19, CD14, and CD56). The samples were then fixed and permeabilised using the Foxp3 Fixation/Permeabilisation concentrate and diluent (eBioscience) and stained with an anti-NFAT1 (Cell Signaling Technology). Sample acquisition was made on an ImageStream X Mark II (Amnis-EMD Millipore, Darmstadt, Germany) with ×40 magnification and analyzed with IDEAS software (v6.0).
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7

Erdr1 Protein Purification and Characterization

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PerCP-Cy5.5-conjugated anti-CD4 (RM4-5), anti-CD3ε (145-2C11), and anti-hamster IgG1 (G94-56) were purchased from BD Biosciences (San Diego, CA, USA). APC-conjugated anti-CD69 (H1.2F3) was obtained from eBioscience (San Diego, CA, USA). Alexa488-conjugated anti-CD4 (GK1.5) was obtained from BioLend (San Diego, CA, USA). Anti-pPLCγ1 and anti-NFAT1 were obtained from Cell Signaling Technology (Danvers, MA, USA). Anti-PLCγ1 was purchased from Santa Cruz Biotechnology (Dallas, TX, USA).
Recombinant Erdr1 was prepared as described previously [38 (link)]. In brief, the bacterial vector with the Erdr1 CDS region was constructed from the Erdr1-pCMV-SPORT6 plasmid (Open Biosystems, Huntsville, AL, USA), and then Erdr1 was purified with over 95% purity from bacteria. Lots with low endotoxin levels (<0.1 EU/mL) determined by the Limulus Amebocyte lysate assay (Cape Cod, East Falmouth, MA, USA) were used for experiments.
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8

ChIP-Seq Analysis of SRC2 and NFAT1

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ChIP was performed with the ChIP-IT High Sensitivity Kit (Active Motif, 53040). Briefly, a total of 2 × 107 CD4+ cells from SRC2fl/fl or SRC2fl/fl/CD4Cre after Treg differentiation were fixed and sheared as described in the ChIP-IT High Sensitivity manual. ChIP reactions were then performed on 30 μg of the prepared chromatin using specific antibodies (anti-SRC2 from Bethyl or anti-NFAT1 from Cell Signaling Technology) overnight, followed by precipitation with protein G agarose beads. DNA was recovered for sequencing or quantitative reverse transcription PCR to quantify specific DNA fragments that were precipitated. For sequencing, ChIP-enriched samples were sequenced on NovaSeq PE100 at TGen. The analysis was performed through Partek Flow. Briefly, the sequence reads were aligned to the mm10 mouse genome with validation of quality through prealignment and postalignment QA/QC. The enrichment of SRC2 binding sites across the genome was analyzed using MACS2. The primers used for RT-qPCR are listed in table S1.
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9

Pancreatic Cancer Cell Lines Characterization

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MiaPaCa-2 and BxPC-3 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). L3.6pl cells were obtained from MD Anderson Cancer Center. All cells were maintained in DMEM (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin in a 5% CO2 atmosphere at 37 °C. The cell lines have been tested and authenticated in a core facility of the Applied Genomics Technology Center at Wayne State University. The method used for testing was short tandem repeat (STR) profiling using the PowerPlex® 16 System from Promega (Madison, WI. USA). RP4010 (Rhizen Pharmaceuticals S.A., La Chaux-de-Fonds, Switzerland) was dissolved in DMSO to make a 50-mM stock solution; 1-mM stock solutions of gemcitabine (Gemzar, Eli Lily, Indianapolis, IN, USA) and nab-paclitaxel (Abraxane, Celgene, Summit, NJ, USA) were also made in DMSO. Anti-NFAT1 (Cell Signaling, Danvers, MA, USA), anti-p-Akt (Cell Signaling), anti-p-4EBP1 (Cell Signaling), anti-S6K (Cell Signaling), anti-p-S6K (Cell Signaling), anti-NF-κB (MilliporeSigma, Burlington, MA, USA), anti-β-actin (Cell Signaling), and anti-GAPDH (Thermo Fisher Scientific, Waltham, MA, USA) primary antibodies were used for Western Blot analysis.
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