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17 protocols using p syk

1

Comprehensive Antibody Panel for Actin Cytoskeleton Analysis

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The following antibodies were used in this study: rabbit anti-myo1e has been previously described77 (link); myo1f (Santa Cruz, B-5, #376534); capping protein (Millipore, #AB6017); Arp3 (Millipore, clone 13C9, #MABT95); BSA (Sigma, clone 3H6, #SAB5300158); rat anti-mouse CD16/32 (BD, #553141); AffiniPure mouse anti-rat (Jackson Labs, 212-005-082); the following antibodies were purchased from Cell Signaling Technologies: pSyk (#2701), Syk (#13198), pAkt (#4060), Akt (#4691), pERK (#4370), ERK (#9102); fluorescent secondary antibodies against mouse or rabbit (Life Technologies). CARMIL1 antibody (WU-C101) was a gift from John Cooper, Washington University in St. Louis (St. Louis, MO).
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2

Western Blot Analysis of BCR Signaling

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Luxeptinib was provided by Aptose Biosciences. Ibrutinib (#HY-10997) was purchased from MedChem Express. Goat anti-human IgM (#109-005-043) was purchased from Jackson ImmunoResearch. Human lymphoma cell lines SU-DHL-6 (#CRL-2959), JeKo-1 (#CRL-3006), RL (#CRL-2261) and Fetal Bovine Serum (#30–2020) were obtained from ATCC. SU-DHL-6 is a human lymphoblast-like cell line, JeKo-1 is a mantle cell lymphoma cell line and RL is a human non-Hodgkin’s lymphoma B cell line. RPMI-1640 medium (#11875–093) and penicillin/streptomycin (#15070063) were purchased from Thermo Fisher Scientific. Antibodies against p-BTK (Y223) (#87141), BTK (#56044), p-PLCγ2 (#3871), p-SYK (#2710), SYK (#80460), p-BLNK (#3601), BLNK (#36438), p-CD79A (#5173), p-LYN/LCK/HCK/BLK (#70926), p-LYN (Y507) (#2731), LYN (#2796, #4576), pSrc family (#6943) and GAPDH (#2118) were purchased from Cell Signaling Technology. Phospho-BTK (Y551) (#ab40770) was purchased from Abcam. PLCγ2 (#sc-5283) and CD79A (#sc-20064) were purchased from Santa Cruz Biotechnology. All other reagents and chemicals used were of analytical grade and were obtained from Sigma-Aldrich or Thermo Fisher Scientific.
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3

Western Blot Analysis of Apoptosis Proteins

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Protein lysates were prepared by resuspending cell pellets in 2X laemmli sample (#161-0737, Bio-Rad Laboratories, Hercules, CA) buffer containing 5% β-mercaptoethanol. The protein lysates were separated by electrophoresis on SDS-PAGE and then electro-transferred onto Polyvinylidene difluoride (PVDF) membranes (Millipore Corp., Bradford, MA, USA). Detection of specific protein was carried out by enhanced chemiluminescence following the manufacturer’s instructions (P90720, Millipore corporation, MA, USA). We used the following primary antibodies: Caspase-9 (#9503, #7237), Caspase-8 (#9746), Caspase-7 (#8438), Caspase-3 (#9664), Bak (#3814), Bax (#2772), Bcl-xl (#2762), p-AKT (#4058), AKT (#2967), p-ERK (#4376), ERK (#4695), p-P38 (#9216), P38 (#8690), p-JNK (#9255), JNK (#9258), p-SYK (#2710), and SYK (#2712) were purchased from Cell Signaling Technology, Inc.. PARP-1 (sc-74470) and β-actin (sc-47778) were purchased from Santa Cruz Biotechnology, Inc.. p-FAK(Y576/577) (ab76244), p21 (ab7960) were purchased from Abcam. p-FAK(Y397) (611722), FAK (611008), and p16 (551154) were purchased from BD Biosciences. Densitometry analyses were performed using Image J software.
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4

Signaling Pathways in BMDC Activation

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BMDCs were washed and resuspended at 6 × 106cells/mL in RPMI‐1640 with L‐glutamine supplemented with β‐mercaptoethanol (50 μM), penicillin/streptomycin (100 μg/mL) for 3 h prior to stimulation with HKCA (6.25 × 105cells/mL) or curdlan (100 μg/mL) at 37°C for 0–20 min. Cells were lysed (1% Triton, 120 mM NaCl, 50 mM Tris, 0.1% SDS, 1 mM EDTA, containing protease/phosphatase inhibitors) and resolved in SDS‐PAGE gels and transferred to PVDF membranes, blocked (Tris, 5% BSA, 0.05% Tween20) and probed with the indicated antibodies; pSyk (clone; C87C1), Syk (clone; D1I5Q), pErk and Erk (mAb Rabbit IgG), Pp38 (clone; D3F9), p38 (clone; D13E1), IκBα (clone; 44D4), pIκBα (clone; 14D4) (all immunoblotting antibodies from Cell Signaling Technologies) followed by anti‐rabbit‐HRP (Dako) secondary antibody. Proteins visualized by SuperSignal chemiluminescent reaction (Pierce) in a ChemiDoc station (BioRad). Densitometry measurements were performed with ImageJ software.
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5

Multi-parameter Flow Cytometry Analysis

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Single-cell suspensions were prepared from spleen, LNs, bone marrow, or peritoneal lavage. After blocking Fc receptors using anti-CD16/32 antibodies, cells were stained with the appropriate combination of the following antibodies: B220 (RA3-6B2), TCRβ (H57-597), CD21 (7G6), CD4 (GK1.5), CD23 (B3B4), CD24 (M1/69), CD43 (S7), Ly-51 (6C3), B and T cell activation antigen (GL7), CD95 (Jo2), CD138 (281.2), IgG1 (A85.1), CD5 (53–7.3), CD11b (M1/70), CD19 (1D3), IgM (1B4B1 or II/41), and IgD (11–26).
For in vivo labeling, 1 µg phycoerythrin-labeled anti-CD45.2 was injected intravenously into recipients. After 2 min, animals were sacrificed.
For staining of intracellular signaling molecules, cells were fixed with 2% formaldehyde and permeabilized with ice-cold methanol for 30 min. Cells were then stained with primary antibodies against pSyk, pSrc, or pAkt, (all from Cell Signaling Technology), and then with secondary 555 anti–rabbit (Life Technologies) or, alternatively, with Alexa Fluor 647–labeled pErk (Phosflow; BD).
Data were acquired on LSR Fortessa (BD) and analyzed with FlowJo (Tree Star).
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6

In Vitro Cell Culture Protocols

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Dulbecco’s modified Eagle’s medium (DMEM), antibiotics (penicillin and streptomycin), and trypsin-ethylenediaminetetraacetic acid (EDTA) were purchased from Gibco BRL (Grand Island, NY, USA). Fetal bovine serum (FBS) was obtained from Biowest (Kansas City, MO, USA), and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), LPS, 4-nitrophenyl n-acetyl-b-d-glucosaminide (p-NAG), and monoclonal anti-DNP-IgE were supplied by Sigma–Aldrich (St. Louis, MO, USA). DNP-BSA was procured from Invitrogen (Gaithersburg, MD, USA). Primary antibodies against p-p38, p38, p-JNK, JNK, p-ERK, ERK, p-Lyn, Lyn, p-Syk, Syk, p-PLCγ, PLCγ, and β-actin were obtained from Cell Signaling Technology (Danvers, MA, USA), and FcεRIγ, from LSBio (Seattle, WA, USA). SensiFAST SYBR No-ROX kit mix was purchased from Biolines (Seoul, Korea), and human filaggrin, AQP3, and HA ELISA kits were obtained from CUSABIO (Seoul, Korea). Rat basophilic leukemia (RBL-2H3, ATCC® CRL-2256) and murine macrophage (RAW264.7, ATCC® TIB-71) cells were procured from the American Type Culture Collection (ATCC), while human immortalized keratinocyte (HaCaT) cells were obtained from Prof. Lee of Chosun University in Korea.
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7

DLBCL Phosphorylated Protein Expression

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The study included 62 DLBCL samples in two tissue microarrays from 2000–2011. Twenty-five cases were from nodal sites and 37 from extranodal sites. Only tumors with enough tissues were included. Immunohistochemical stains of p-STAT3 (Y705, rabbit monoclonal Ab, clone D3A7, Cell Signaling) and p-SYK (Y525/526; rabbit polyclonal Ab; Cell Signaling) were performed and the results were evaluated by proportion of lymphoma cells that were stained. The antibody reactivity in ≥ 30% of the lymphoma cells was considered positive. Paraffin-embedded normal tonsil tissue was included as a baseline expression level for p-STAT3 and p-SYK.
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8

Molecular Signaling Pathway Profiling

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Cr-ME was purchased from the Plant Diversity Research Center (DaeJeon, South Korea). Sodium dodecyl sulfate (SDS), 3-(4,5-dimethylthiazol,2-yl)-2,5-diphenyltetrazolium bromide (MTT), polyethylenimine (PEI), dimethyl sulfoxide (DMSO), polyinosinic: polycytidylic acid (Poly (I:C), and lipopolysaccharide (LPS, Escherichia coli O111:B4) were obtained from Sigma Chemicals Co. (St. Louis, MO, USA). Cell culture chemicals such as fetal bovine serum (FBS) was purchased from Biotechnics Research (Lake Forest, CA, USA), and Roswell Park Memorial Institute 1640 (RPMI 1640) and Dulbecco’s Modified Eagle Medium (DMEM) were obtained from HyClone (Grand Island, NY, USA). The RAW264.7 cell line (No. TIB-71) and human embryonic kidney cell line (HEK293T) (No. CRL-3216) were acquired from the American Type Culture Collection (ATCC, Rockville, MD, USA). Luciferase constructs with NF-κB and the PDR (III-I) luciferase promoter were used as previously reported [53 (link)]. Phospho- and total antibodies against p50, p65, Src, p-Src, Syk, p-Syk, IκBα, p-IκBα, IRF3, TBK1, and β-actin were purchased from Cell Signaling Technology (Beverly, MA, USA) and Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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9

Protein Detection by Western Blot

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Total protein from cells and kidney were isolated by RIPA buffer for western blot analysis as previously described 8 (link)-11 (link), 35 (link). Primary antibodies against NPY, Y1R, phospho (p)-NF-κB/p-p65, NF-κB/p65, p-Syk (all from Cell Signaling), iNOS (Abcam, Cambridge, UK), Mincle (Santa Cruz or MBL International, Woburn, MA), and β-actin (Santa Cruz) were used. After being stained and washed, the membranes were incubated with LI-COR IRDye 800 conjugated secondary antibodies (Rockland Immunochemicals, Gilbertsville, PA) in the dark for 1 hour. Signals were then scanned and visualized by the Odyssey Infrared Imaging System (Li-COR Biosciences, Lincoln, NE). The ratio of the targeted protein was subjected to β-actin and quantified with ImageJ software (NIH, Bethesda, MD).
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10

Protein Extraction and Western Blotting

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For protein extraction, tissues were homogenized in ice-cold RIPA buffer. Total protein was quantified using the DC Protein Assay according to the manufacturer’s instructions (BioRad, Hercules, CA). Western blotting was performed as previously described with minor modifications13 (link). Briefly, 10 % Bis-Tris polyacrylamide gels (NuPage, Invitrogen) were equiloaded with 10–30μg of protein, electrophoresed at 200V, and electrotransferred to PVDF membranes. After blocking with 5% BSA, membranes were probed with primary antibodies to β-actin (8H10D10), p53 (7F5), PLC-γ (polyclonal), p-PLC-γ (polyclonal), Bcl-XL (54H6; all Cell Signaling), JNK (2C6), p-JNK (G9), Smad4 (polyclonal), p16 (polyclonal), c-Myc (9E10), CARD9 (polyclonal), Syk (polyclonal), p-Syk (polyclonal), Rb (C-15; all Cell Signalling), Dectin-1 (polyclonal; Abcam), Galectin-9 (polyclonal), and Dectin-1 Fc (fc-mdec1a; InvivoGen). Blots were developed by ECL (Thermo Scientific, Asheville, NC). RNA extraction was performed using the RNeasy Mini kit (Qiagen, Germantown, MD) as per manufacturer’s instructions. For Nanostring analysis, the nCounter mouse inflammation panel was employed using the nCounter Analysis System (both Nanostring, Seattle, Washington).
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