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39 protocols using ab 105 c

1

Immunoblotting of EphA2 and Associated Proteins

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The reagents used were as follows: antibodies against EphA2 (6997, CST, Massachusetts), α -tubulin (sc-8035, Santa Cruz, Texas), β -actin (66009-1-Ig, Proteintech, Chicago), Myc-tag (16286-1-Ig, Proteintech, Chicago), Flag-tag (66008-1-Ig, Proteintech, Chicago), Flag-tag (F4049, Sigma-Aldrich, Germany), normal rabbit IgG (AB-105-C, R&D, Minnesota), the horseradish peroxidase (HRP)-conjugated goat-anti-mouse/rabbit secondary antibodies (#31460, #61–6520, Invitrogen, California), IgG (AB-105-C, R&D, Minnesota) and 2,5-dimethylpyrrolyl benzoic acid derivative (sc-314230, Santa Cruz, Texas). All other reagents were obtained from Sigma-Aldrich unless otherwise indicated.
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2

Quantifying IFNAR1 Expression in Abdominal Aortic Aneurysms

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Non-aneurysmal human abdominal aortae were obtained from two organ donors. Infrarenal human AAA specimens were obtained from patients undergoing open surgical repair (n = 6). Collection and use of these specimens were approved by the Human Subject Research Review Board at Xiangya Hospital, Central South University School of Medicine, Changsha, Hunan, China. Non-aneurysmal and aneurysmal mouse aortae were prepared via intra-infrarenal aortic infusion of phosphate-buffered saline (non-aneurysmal) and PPE (aneurysmal), respectively (n = 3 mice/group). All human and mouse aortae were fixed with 4% paraformaldehyde, embedded in paraffin and sectioned (4 μm). Sections were stained with a rabbit anti-IFNAR1 polyclonal antibody (ab244357, Abcam, Waltham, MA, USA) or purified normal rabbit IgG (AB-105-C, R&D Systems, Minneapolis, MN, USA), and detected with mouse- and rabbit-specific HRP (house radish peroxidase)/DAB (3,3′-diaminobenzidine) detection kits (ab64264, Abcam, Waltham, MA, USA) as described previously [22 (link),31 (link)]. IFNAR1 expression was quantified as the percentage of positive staining area with the total aortic cross-sectional (ACS) area using Image J Fuji software (Ver 2.0.0-rc-43/1.53m).
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3

ChIP-qPCR Assay for p63 Regulation

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ChIP-qPCR assays were performed on murine embryonic fibroblasts isolated from p63 flox/flox (f/f) mice (gift of Dr. Elsa Flores; Moffitt Cancer Center & Research Institute), as previously described8 (link). Briefly, cells were seeded onto 150 mm dishes at density of 106 cells/dish, and treated 24 h later with adenoviral vectors expressing GFP or Cre recombinase (AdGFP and AdCre; 150 moi). These cells were collected seven days later and processed using ChromaFlash Chromatin Extraction kits (p-2001; Epigenetek) per manufacturer’s protocol. ChIP was then conducted using H3K27Ac antibody (ab4729; Abcam), HDAC1 antibody (815104; Biolegend) or normal rabbit immunoglobulin G (AB-105-C; R&D systems), as previously described27 (link). ChIP-qPCR was performed using primers synthesized by Sigma Aldrich (Supplemental Table S2). Fold-enrichment of PCR products was calculated after normalization with input of all three types of infected cells.
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4

Syngeneic Mouse Tumor Model with NK Depletion

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1 x 105 7940b tumor cells were mixed with 5 x 105 fibroblasts, resuspended in a 50:50 mix of serum-free media [DMEM+1% Pen/Step] and Matrigel (Corning 354234). Two fibroblast clones (in equal numbers) were used in each injection to reduce the impact of clonal variability. Cells were injected subcutaneously into the flanks of NU/J mice (Jackson Laboratory Stock No: 002019). Tumors were measured every other day with calipers, and animals were sacrificed after 10 days. For NK cell depletion experiments, 10μl of anti-asialo GM1 (Wako 986–10001) or an equivalent volume of normal Rabbit IgG control (R&D AB-105-C) was diluted 1:10 in sterile PBS and injected intraperitoneally. Injections were given 24h before tumor implantation, on the day of tumor implantation, and once every three days for the remainder of the experiment.
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5

Transwell Migration Assay for BMSC and MB Cells

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Migration assays were carried out in a 24-well transwell system equipped with porous (8 μm) polycarbonate membranes. 2 × 105 MB cells were resuspended in 600 μL of growth medium supplemented with 1% FBS and plated into the lower chamber of the transwell system; 5.0 × 104 BMSC cells were resuspended in 200 mkl of growth medium supplemented with 1% FBS and plated into Transwell inserts which were then placed into another transwell system with the lower chamber filled with 600 μl of serum-free medium. After 24 hours the cells on the inserts or in lower chambers were transfected as indicated, 6 hours after the transfection the media was changed and the inserts with BMSC, were placed into the wells with MB cells and incubated at 37 °C for 24 h. When indicated, CXCR4 (Abcam, #ab10403) or SDF1 (CXCL12) (Abcam, #ab9797) antibodies were added to the medium at 10 mkg/ml and 4 mkg/ml concentrations respectively. The inserts were then discarded, and upper sides of the filters were swabbed to remove the cells that did not cross the membrane. The cells present on the lower side of the filters were then fixed in 4 % paraformaldehyde, stained with DAPI and the counted under the microscope. All the experiments were performed in duplicate. The following control antibodies were used: rabbit IgG control (AB-105-C, R&D systems) and mouse IgG2b isotype control (MAB004, R&D systems).
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6

Immunohistochemical Analysis of ALK5 and FOXO1 in Mouse Knee Joints

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Knee joints from mice were fixed with 4% paraformaldehyde (PFA) (Wako Pure Chemical Industries) for 2 days, decalcified with K-CX (FALMA, Tokyo, Japan) for 2 days, and embedded in paraffin. Sections were cut into 4 μm–thick sections, deparaffinized, and rehydrated; antigen retrieval was performed by incubation overnight with ethylenediaminetetraacetic acid (EDTA) (1 mM) at pH 8.0. Endogenous peroxidase activity was blocked by incubation with 3% hydrogen peroxidase (H2O2) in methanol for 30 minutes. After blocking with normal horse serum (Vectastain Universal Elite ABC kit; Vector Laboratories, Burlingame, CA, USA) for 30 minutes, sections were incubated with antibodies against ALK5 (sc-398; Santa Cruz Biotechnology), FOXO1 (#2880; Cell Signaling Technology) and normal rabbit IgG (AB-105-C; R&D Systems, Minneapolis, MN, USA) for 1 hour. Sections were incubated with biotinylated secondary antibodies for 30 minutes, followed by incubation with streptavidin–peroxidase complex (Vectastain Universal Elite ABC kit) for 30 minutes. Antibody complexes were visualized using the diaminobenzidine substrate system (Wako Pure Chemical Industries), and counterstained with hematoxylin. The percentage of cells positive for ALK5 and FOXO1 was determined using the BZ-II Analyzer software (Keyence, Osaka, Japan).
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7

Immunofluorescence Staining of Smooth Muscle Cells

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Cells were washed with PBS, fixed in 4% PFA for 15 min, and permeabilized for 10 min in 0.5% [v/v] Triton X-100 (Sigma Aldrich). After blocking in 1% bovine serum albumin (BSA), fixed and permeabilized SMCs were incubated with anti-human alpha-smooth muscle actin (α-SMA; 1:200, Dako, M0851), TOM20 (1:200, Proteintech, 11802-1-AP), alpha-tubulin (α-tubulin, 1:25, Cell Signaling, 2144S), calponin (1:50, Thermo Scientific, MA5-32061), mouse IgG control (DAKO, X0931), or rabbit IgG control (R&D systems, AB-105-C). Subsequently, after washing Alexa Fluor 594 (1:1000, Thermo Scientific, R37115) or 488 (1:1000, Life Technologies, A32723) labeled secondary antibody was applied. Nuclei were counterstained with 2.5 μg/ml 4′,6-Diamidino-2-phenylindole dihydrochloride (DAPI, Carl Roth), and slides were covered using a mounting medium (Dako).
For mitochondrial visualization, cells were labeled with 300 nM MitoTrackerRed FM (ThermoFisher Scientific) in serum-free CM at 37°C for 30 min. Nuclear staining was performed with 1 μM Hoechst 33,342 solution (Thermo Scientific). Images were acquired using a Leica DMI6000B inverted fluorescence microscope.
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8

Quantifying Histone Modifications in Thymocytes

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Chromatin was prepared from total thymocytes of 3-4 week old Rag2−/− or homozygous 15-12 Rag2−/− mice and was immunoprecipitated using antibodies specific for acetylated histone H3 (H3ac; Millipore, 06-599), trimethylated histone H3 lysine 4 (H3K4me3; Abcam, ab1012) or control rabbit IgG (R&D systems, ab-105-c) following a protocol described previously (13 (link)). Immunoprecipitated and input samples were quantified by SYBR Green real-time PCR as above. Experimental values were expressed as bound/input and were normalized to values for β2-microglobulin (B2m) in each sample.
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9

Retina Tissue Immunoprecipitation and RAGE Detection

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Retina tissue was homogenized in 30 mM of Tris-HCl lysis buffer (pH 7.5) containing 10 mM EGTA, 5 mM EDTA, 1% Triton X-100, 250 mM sucrose, 1 mM NaF, 1 mM phenylmethylsulfonyl fluoride, 1 mM Na3VO4, and protease inhibitor. Protein (150µg) was incubated overnight at 4 °C with 2 µg of the anti-S100A4 antibody and the normal rabbit IgG control antibody (Cat. No. AB-105-C, R&D Systems). Prewashed protein A/G plus agarose beads (20 μl of bead slurry; Santa Cruz Biotechnology, Inc.) were then added to the mixture and rolled for 1 h at 4 °C. After centrifugation, immunoprecipitates were washed 4X with lysis buffer. After the last wash, the resultant pellets were resuspended in 20 μl of 2X Laemmli’s sample buffer and then denatured for 5 min at 95 °C, separated by gel electrophoresis, and transferred to polyvinyl difluoride membranes. This was followed by immunoblotting with an anti-RAGE antibody (1:500; sc-5563; Santa Cruz Biotechnology Inc.) and detection with chemiluminescence plus a Luminol HRP substrate. To evaluate the lane-loading control, the blots were stripped and the S100A4 protein was detected with the anti-S100A4 antibody.
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10

Chromatin Immunoprecipitation (ChIP) Protocol

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6-8 × 106 thymocytes were cross-linked in 1ml RPMI containing 10% fetal bovine serum and 1% paraformaldehyde for 10 min at 25 °C. Cross-linked thymocytes were washed in PBS, pelleted and incubated in 1 ml of 5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% NP-40 for 10 min on ice, after which they were disrupted by Dounce homogenization using 15 strokes with pestle “A”. Nuclei were precipitated, washed, and lysed in 500 μl of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS. Chromatin was sheared using a Sonicator 3000 (Qsonica) for 4.5 min (six cycles of 15 s on, 30 s off at power=2). For one ChIP experiment, 200 μl sonicated chromatin was diluted 10-fold and precipitated with 5 μl anti-CTCF (07-729; Millipore) or anti-H3Ac (06-599; Millipore) or 5 μg control rabbit IgG (ab-105-c; R&D Systems). Immune complexes were isolated with Protein A agarose/salmon sperm DNA (Millipore), washed, eluted and incubated at 65 °C for 4 h to reverse cross-links. DNA was purified by phenol:chloroform extraction and isopropanol precipitation. Enrichment of chromatin was measured by qPCR as previously described14 (link) with primers listed in Supplementary Table 1. Data from CTCF-ChIP and H3ac-ChIP were expressed as bound/input and then normalized to values for Myc and B2m, respectively.
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