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N-Myc is a protein that plays a crucial role in regulating cell growth and development. It is a member of the Myc family of transcription factors, which are important for controlling the expression of genes involved in cellular processes such as proliferation, differentiation, and apoptosis. N-Myc is particularly important in the development of certain types of cancer, such as neuroblastoma, and is often used as a biomarker to help diagnose and monitor the progression of these diseases.

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28 protocols using n myc

1

Comprehensive Antibody Panel for Oncogenic Signaling

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The following antibodies were used: N-MYC (9405), N-MYC (51705), cleaved PARP (9541), cleaved caspase 3 (9661), ALK (3333), AKT (4691), pAKT-T308 (9275), pAKT-S473 (#9271), ERK (4695), pERK (4377), S6 (2217), pS6 (4857), STAT3 (4904), pSTAT3 (9131), ABCB1 (12683), SOX2 (3579), β-actin (4967), CTCF (3417), normal rabbit IgG (2729) and HRP anti-mouse IgG (7076) from Cell Signaling Technology; HRP anti-rabbit IgG (sc-2357) from Santa Cruz Biotechnology; BRD4 (A301–985A100) and SMC1A (A300–055A) from Bethyl Laboratories; CTCF (07–729), SOX9 (AB5535) and H3K27me3 (07–449) from Millipore; pALK-Y1507 (ab73996), BORIS (ab187163) and H3K27ac (ab2729) from Abcam; BORIS (NBP2–52405) from NOVUS Biologicals; BORIS (39851) from Active Motif; SIX1 (HPA001893) from Sigma-Aldrich; and Vysis LSI N-MYC (2p24) SpectrumGreen/Vysis CEP 2 SpectrumOrange Probe (07J72–001) from Abbott.
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2

Western Blotting of N-Myc and β-Actin

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Western blotting was performed as previously described [19 (link)]. Briefly, 60 µg of total protein was separated on 10% polyacrylamide/SDS gel and transferred to PVDF membranes, and the membranes were blocked with 5% (w/v) bovine serum albumin (BSA) in tris buffered saline (TBS) (+0.1% Tween-20). The primary antibodies included N-Myc (Cell Signaling Technology Cat # 84406, RRID: AB_2800038, Danvers, MA, USA), β-Actin (Cell Signaling Technology Cat # 4970, RRID: AB_2223172), and horseradish peroxidase-conjugated secondary antibody: anti-rabbit IgG (Cell Signaling Technology Cat# 7074, RRID: AB_2099233).
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3

Investigating Neuroblastoma Targeted Therapies

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JQ1 and ABT-263 were purchased from Selleck chemical (Shanghai, China) and stock solutions were prepared in DMSO (Sigma–Aldrich, Saint Louis, MO, USA) at a concentration of 10 mM. Antibodies against p21, Bcl-2, N-Myc, c-Myc, Bim, PARP, cleaved-Caspase 3 and Mcl-1 were from Cell Signaling Technology, Danvers, MA, USA. Ki67 antibody was from ZSGB-BIO, Beijing, China. Actin antibody was from TransBionovo, Beijing, China. The siRNA #1 and #2 against human Bim as well as its negative control siRNA were purchased from Cell Signaling Technology (Danvers, MA, USA). And the siRNA #1 against human N-Myc as well as its negative control siRNA were purchased from Santa Cruz Biotechnology, Dallas, Texas, USA. The siRNA #2 against human N-Myc as well as its negative control siRNA were pruchased from OriGene Technologies, Rockville, MD, USA.
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4

Antibody Characterization for Cell Signaling

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Antibody against CDC42 was purchased from Cytoskeleton, Inc. (Denver, CO) and Santa Cruz Biotechnology, Inc. (Santa Cruz, CA). Antibody against AKT2, AKT, survivin, N-myc, cleaved caspase-3, cleaved PARP and cell lysis buffer were obtained from Cell Signaling Technology (Beverly, MA). Twist antibody and horseradish peroxidase (HRP)-conjugated secondary antibodies against mouse and rabbit IgG were obtained from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA). Anti β-actin monoclonal antibody and fetal bovine serum (FBS) were from Sigma-Aldrich (St. Louis, MO). NuPAGE Novex 4–12% Bis–Tris Gel and Lipofectamine 2000 were purchased from Invitrogen (Carlsbad, CA). Cell Counting Kit-8 (CCK-8) was purchased from Dojindo Molecular Technologies, Inc. (Santa Clara, CA). Agarose (SeaPlaque®) was from Lonza Inc. (Allendale, NJ). Cell Death Detection ELISAPlus was purchased from Roche Applied Science (Indianapolis, IN).
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5

Comprehensive Western Blotting Procedure

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The primary antibodies for western blotting were n-Myc (cat #9405S), Gab2 (cat #3239S), Bim (cat #2819S), SHP2 (cat #3397T), phospho-SHP2 (Y542, cat #3751S), Akt (cat #4691S), phospho-Akt (T308, cat #4056S), phospho-Akt (S473, cat #4060S), S6 Ribosomal protein (cat #2217S), phospho-S6 Ribosomal protein (S235/236, cat #4858S), phospho-S6 Ribosomal protein (S240/244, cat #5364S), Erk (cat #4695S), phosphor-Erk (cat #4370S), NF1 (cat #14623S), cleaved PARP1 (cat #9541S), cleaved Caspase3 (cat #9664S), β-Actin (cat #4967S); all these antibodies are from Cell Signaling Technology (Beverly, MA). The GAPDH antibody (Wong et al., sc-32233) from Santa Cruz Biotechnology (Dallas, TX) was used as a loading control. The secondary antibodies used were anti-mouse IgG (GE Healthcare Life Sciences, cat #NXA931) and anti-rabbit IgG (GE Healthcare Life Sciences, cat #NA934). SHP099 (Wong et al., M6314) was from Abmole (Houston, TX), Trametinib (GSK 1120212, cat #CT-GSK212), RMC-4550 (Wong et al., CT-RMC4550) and TNO-155 (Wong et al., CT-TNO-155) were from ChemiTek (Indianapolis, IN). AZD-2014 was from Selleckchem (Wong et al., S2783). Crystal violet was from Thermo Scientific (cat #42583-0250).
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6

Western Blot Analysis of Cellular Signaling Pathways

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Western blot assays were performed as previously described (24 (link)). Briefly, proteins (20 μg/sample) were separated using SDS–polyacrylamide gel electrophoresis and electroblotted to nitrocellulose membranes (Bio-Rad). Membranes were probed overnight with the following antibodies: phosphor-AKT (Ser 473), phosphor-AKT (Thr 308), AKT, N-MYC, phosphor-ACC (Ser 79), ACC, phosphor-GSK3b (Ser 9) GAPDH (obtained from Cell Signaling Technology), NAMPT, NAPRT (obtained from GeneTex) or α-tubulin (obtained from Abcam). Membranes were then washed, reacted with horseradish peroxidase–conjugated secondary antibodies and visualized using enhanced chemiluminescence (Thermo Scientific). Relative levels of NAMPT and NAPRT as well as quantitation of cleaved caspase 3 (active) and parp cleavage (indicative of caspase activation) were determined using Image J (imagej.nih.gov).
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7

Immunoblot analysis of cellular signaling

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Cells were lysed in lysis buffer (25 mM Tris pH 8.0, 125 mM NaCl, 1 mM MgCl2, 1% Triton X-100, 1 mM sodium orthovanadate, 1 mM sodium fluoride, 1X protease inhibitor (Sigma-Aldrich), phosphatase inhibitor cocktails #2 and #3 (Sigma-Aldrich), and 1 mM PMSF). Cell lysates were resolved on a Nupage 4-12% Bis-Tris gradient gel (Life Technologies) and probed using antibodies recognising phospho- and total eIF4E1 (Cell Signaling #9741 and Santa Cruz sc-9976), phospho- and total ERK (#9101 and #9102, Cell Signaling), c-Myc (#9402), n-Myc (#9405), p-MNK1/2 (#2111), dicer (#3363), eIF4A (#2013) (Cell Signaling), GAPDH (ab8245), BTK (ab54219), YY1 (ab12132) (Abcam), eIF4E3 (Proteintech: N-terminal, #17282-1-AP), MNK1 (sc-6965), MNK2 (sc-6964), CDK6 (sc-7961), eIF4G (sc-11373), MCL-1 (#sc-819) (Santa Cruz) or GFP (EVN-AB513, Axxora). All primary antibodies were used at 1: 1,000 dilution. Densitometry analyses were performed using ImageJ software (NIH) and presented as ratio of target band signal intensity to GAPDH band signal intensity. Full immunoblots are presented in Supplementary Fig.10.
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8

Antibody Validation for Neuropathology

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Antibodies used in this study were the following: Actin (1:1000, Santa Cruz, sc-1615), Arid1a (1:1000, Cell Signaling, #12354), Chd5 (1:1000, ThermoFisher Scientific, #PA5-37148), Gfap (1:200, Abcam, ab7260), Ki67 (1:1,000, Abcam, ab15580), N-Myc (1:1000, Cell Signaling, #9405), Synaptophysin (1:100, ThermoFisher Scientific, #RM-9111-S), S100 (1:500, Abcam, ab868), Th (1:250, Millipore, AB152) and Tuj1 (1:1000, Abcam, ab18207).
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9

Western Blot Protein Detection Protocol

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Cell lysates and tissues were homogenised in RIPA buffer (50 mM TRIS-HCl pH 7.4, 150 mM NaCl, 1% NP-40, 0.1% SDS, 5 mM EDTA) supplemented with a protease and phosphatase inhibitor cocktail (Roche). To terminate the reaction, SDS sample buffer [125 mM Tris- HCl (pH 6.8), 6% SDS, 20% glycerol, and 0.02% bromophenol blue supplemented with 10% β-mercaptoethanol] was added and the samples boiled for 10 min. Proteins were separated on SDS-PAGE 8 to 12% Tris-glycine gels (Life Technologies) and transferred to a nitrocellulose membrane (BioRad). For protein detection, membranes were incubated in 3% BSA in TBS/0.05% Tween-20 blocking buffer for 1 h at room temperature, and incubated overnight at 4 °C with primary antibodies from Cell Signaling Technology®: Phospho-FGFR(Y653/654) (#3471), Phospho-Src Family(Y416) (#2101), N-Myc (#9405), Phospho-Akt(T308) (#9275) and GAPDH (#5174), the latter used as a loading control. The following day, membranes were incubated with HRP-conjugated secondary antibodies (Cell Signaling Technologies) at a 1:40000 dilution in 0.75% BSA in TBS/0.05% Tween-20 buffer for 1 h at room temperature. Signal was detected using the chemiluminescent detection reagent Amersham ECL Prime Western Blotting Detection Reagent (GE Healthcare Life Sciences) and imaged using BioRad ChemiDoc XRS+.
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10

Immunoblotting Assay for Protein Expression

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Cells were lysed in radioimmunoprecipitation buffer (Boston Bioproducts) with a cocktail of protease and phosphatase inhibitors (Roche). 12.5 µg of protein was separated by 4–20% SDS-PAGE and transferred to polyvinylidene difluoride membranes by electroblotting. After blocking with 5% nonfat dry milk in TBST (20 mM Tris [pH, 7.5], 150 mM NaCl, 0.1% Tween20), membranes were incubated at 4C overnight with primary antibodies. After washing and incubation with horseradish peroxidase-conjugated secondary antibodies (Cell Signaling Technology), blots were washed, and signals were visualized with an ECL kit (Amersham Bioscience). Primary antibodies: c-Myc, N-Myc, Hexokinase II (HKII), PKM2, LDHA, cleaved-PARP, phospho-AMPK, phospho-Raptor, phospho-mTOR, phospho-S6, phospho-4E-BP1, Cleaved PARP, actin (Cell Signaling); NAMPT (Bethyl Laboratories); Naprt1 (Sigma Aldrich); and Vinculin (Thermo Scientific).
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