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10 protocols using m5670

1

Western Blot Analysis of MAPK Signaling

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Cortical and hippocampal samples were homogenized in lysis buffer (50 mM Tris–HCl, pH 8.0, 50 mM NaCl, 1% Triton-X100, 1 mM DTT) supplemented with protease and phosphatase inhibitor cocktails (Roche) at 4 °C, and the lysates were subjected to SDS-PAGE analysis. Gels were transferred to nitrocellulose membranes and probed with the following antibodies: diphosphorylated Erk1/2 (1:1000; M8159, RRID: AB_477245, Sigma Aldrich), Erk1/2 (1:50,000; M5670, RRID: AB_477216, Sigma Aldrich), phospho-p38 MAPK (1:500; 4511S, RRID: AB_2139682, Cell Signaling Technology), p38 MAPK (1:1000; 9212S, RRID: AB_330713, Cell Signaling Technology), phospho-JNK1/2/3 (1:2000; MABS740; Merck Millipore), JNK1/23 (1:2000; 10023-1-AP, RRID:AB 2281669, Proteintech Group), occludin (1:1000; 40-4700, RRID: AB_2533468, Thermo Fisher Scientific), and β-actin (1:100,000, NB600-501, RRID: AB_10077656, Novus Biologicals). PageRuler Plus Prestained Protein Ladder (#26619, Thermo Scientific) was used as the molecular weight marker. Blots were quantified using Fiji-ImageJ software. The densitometry data were normalized either to the total form of the corresponding kinase or to β-actin.
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2

Western Blot Quantification of Cellular Signaling Proteins

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The MCF-7 cell line was maintained under standard conditions in Dulbecco's modified Eagle's medium supplemented with 10% foetal bovine serum. Cells were washed with ice cold phosphate buffered Saline and lysed in RIPA buffer (1% NP-40, 0.1% SDS, 0.5% Sodium deoxycholate, 50 mM Tris pH 7.5, 150 mM NaCl) supplemented with protease and phosphatase inhibitor cocktails (Sigma Aldrich) and protein concentration was quantitated by BCA protein assay (Invitrogen). Purified BSA (Applichem) was dissolved in RIPA buffer. Cell lysates and a BSA sample were serially diluted 1∶2 and run on SDS-PAGE using a standard protocol. Proteins were transferred to the PVDF (for ECL based detection) or Nitrocellulose (for LI-COR based proteins detection) membranes. Membranes were blocked with blocking solution (11500694001, Roche) for BSA detection or 5% skimmed milk for rest of the membranes. For Western blotting ERK (M-5670, Sigma Aldrich), mTOR (2972, Cell Signaling Technology), RSK1 (sc-231, Santa Cruz) and BSA (sc-50528, Santa Cruz) antibodies were used. Anti-rabbit HRP-conjugated (Cell Signaling Technology) or anti-Rabbit IR 800 (LI-COR) secondary antibodies were used for ECL or LI-COR protein detection systems, respectively. Signal was detected by standard X-ray films (Fuji), CCD camera (Advanced Molecular Vision) or LI-COR scanner.
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3

Immunostaining and Western Blot for GABA Receptor

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Mouse CaMKIIβ (1:1500 for Western blotting [WB] and 1:150 for in situ proximity ligation assay [PLA], ThermoFisher Scientific #13-9800, Basel, Switzerland), mouse GABAB1 (1:250 for immunofluorescence staining [IF] and, 1:100 for PLA; Abcam #ab55051), rabbit GABAB1bN directed against the N-terminus of GABAB1b (affinity-purified,1:100 for IF; custom made by GenScript), rabbit GABAB2N directed against the N-terminus of GABAB2 (affinity-purified, used for cell surface staining, 1:25 for IF; custom made by GenScript), rabbit GABAB2 (1:500 for IF, 1:100 for PLA, 1:800 for Western blotting; Abcam #ab75838, via Lucerna-Chem AG, Luzern, Switzerland), mouse phospho-serine (1:150 for PLA, Sigma-Aldrich #P5747), mouse phospho-threonine (1:150 for PLA, Millipore #708014, Darmstadt, Germany), rabbit ERK1/2 (1:500 for WB and IF, 1:100 for PLA, Sigma-Aldrich #M5670), mouse pERK1/2 (1:250 for WB and IF, Sigma-Aldrich #M9692), rabbit HA (1:500 for IF, Sigma-Aldrich #SAB5600116). For immunofluorescence staining, secondary antibodies used were labeled with Alexa Fluor Plus 488, 555, or 647 (1:2000, ThermoFisher), and for Western blotting, antibodies were conjugated to IRDye 700CW or IRDye800CW (LI-COR Biosciences, Bad Homburg, Germany).
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4

Antibody Immunohistochemistry for Cell Markers

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The following antibodies were used: mouse monoclonal antibodies to β gal
(1:1,000, G8021, Sigma), pERK (1:50, sc-7383, Santa Cruz), CC1 (1:50, OP80,
Millipore), neurofilament (1:1,000, NE1017, Millipore), and rabbit polyclonal
antibodies to Olig2 (1:500, AB9610, Millipore), ki67 (1:500, SP6, Cell Marque),
Caspr (1:1,000) (ref. 68 (link)), pERK (1:1,000, 4370P,
Cell Signaling), ERK (1:2,000, M5670, Sigma), GPR17 (1:20, Cayman Chemical,
17087), and goat polyclonal antibody to GPR37 (1:50, Santa Cruz, sc-27548), and
rat monoclonal antibodies to MBP (1:300, MAB386, Chemicon), PDGFRα
(1:1,000, APA5, BD Pharmingen), and hybridoma supernatants of mouse anti-O4
(1:5) and rat anti-PLP (1:10, AA3). Secondary antibodies were obtained from
Jackson Immunoresearch and Invitrogen. PLX4032 (ref. 41 (link)) and myr-EPE (ref. 40 (link)) are
generous gifts from Prof. Rony Seger (Weizmann Institute of Science, Rehovot,
Israel). SQ 22536, IBMX and ESI-09 were purchased from Sigma. cAMP levels were
determined by ELISA according to the manufacturer's protocol (cAMP
ELISA kit, Enzo Life Sciences).
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5

Antibodies for Protein Localization and Expression

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Commercially available primary antibodies used in this study for immunoprecipitation (IP), immunofluorescence (IF), proximity ligation assay (PLA), Western blot (WB), and Simple Western capillary system (WES) were as follows: anti-GFP (abcam, ab6556, IF & WB 1:5000, PLA 1:2000), anti-NFH (abcam, ab72996, 1:2000), anti-Actin (MP, clone C4, 08691001, WB 1:5000), anti-GAPDH (Santa Cruz Biotechnology, sc-32233, WB 1:5000), anti-ERK1/2 (Sigma, M5670, WB 1:30000), anti-β-III tubulin TUJ1 (abcam, ab18207, IF 1:1000, WB: 1:6000), anti-Dynein heavy chain (DYNC1H1, Proteintech, #12345-1-AP, PLA 1:50), anti-importin beta 1 (MBS713065, rabbit, polyclonal, 1:1000), and rabbit anti-nucleolin (ProteinTech, 10556-1-AP, 1:100 for IF).
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6

Hippocampal Protein Expression Analysis

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Dorsal hippocampi were collected around the tips of the hippocampal cannulas. Tissue was lysed in modified RIPA buffer, incubated 15 min on ice, and centrifuged for 15 min (15,000g) at 4 °C. Samples were subjected to SDS-PAGE (10 μg per well) and transferred to PVDF membrane (Millipore). Membranes were blocked with I-block (Tropix), incubated with primary antibody overnight at 4 °C, and with secondary antibody for 1 h at 20–22 °C. Bands were detected using alkaline phosphatase chemiluminescence. Primary antibodies used were against β-tubulin (1:4,000, T4026, Sigma), KCC2 (1:2,000, MABN88, Millipore), GABRA4 (1:1,500, sc-20917, Santa Cruz), GABRB2 (1:1,500, ab8340, Abcam), pPKCα/β II (1:800, T638/641), pPKCβ II (1:800, S660), pPKCθ (1:800, T538), pPKCδ/θ (1:800, S638/676) (PKC Sampler kit #9921, Cell Signaling), synapsin-2 (1:1,000, NB 120-13258, Novus Biologicals), NR1 (1:6,000, sc-9058, Santa Cruz), NR2A (1:1,000, 07-632, Millipore), NR2B (1:2,000, ab65783, Abcam), PKA (1:20,000, ab76238, Abcam), CaMKII (1:6,000, C6974, Sigma), Erk-1/2 (1:4,000, M5670, Sigma). All antibodies gave bands at the predicted molecular sizes and were validated by preadsorption experiments with immunogenic peptides used for their production. We also validated the Erk and NR2A antibodies with tissue of knockout mice (data not shown).
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7

Western Blot Analysis of Protein Expression

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Protein samples (30 μg) from cultured cells or aortic specimens were electrophoresed on a 12% polyacrylamide gel by SDS-PAGE and blotted onto a nitrocellulose membrane. After being blocked with 5% BSA for 2 h at room temperature, the membrane was incubated overnight at 4 °C with primary antibodies (PRS3901, M5670, SAB4500491, and SAB4502398; 1:1,000 dilution; Sigma-Aldrich), washed with TBST 3 times, incubated with anti-rabbit secondary antibody (1:5,000 dilution) for 1 h at room temperature and then washed with TBST 3 times.
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8

Western Blotting and qRT-PCR Analyses

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Western blotting and quantitative RT-PCR (RT-qPCR) were performed as previously described [45 (link)]. Antibodies used were TrkB (1/1,000 dilution, #4603, Cell Signaling Technologies) and ERK1/2 (1/10,000 dilution, M5670, Sigma Aldrich). TaqMan assays (Applied Biosystems) used were DKK1 (Hs00183740_m1*), EGR1 (Hs00152928_m1*), FZD7 (Hs00275833_s1*), RET (Hs01120030_m1*), NTRK2 (Hs00178811_m1*), c-MYC (Hs00905030_m1*), MYCN (Hs00232074_m1*), ASCL1 (Hs04187546_g1), LMO4 (Hs01086790_m1) and the endogenous control genes RPLPO (4310879E) and ACTB (β-actin, 4326315E). Biological duplicates were generated for all samples; technical replicates for every sample were also performed.
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9

Quantitative Analysis of Activated MAP Kinases

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S2 cells were collected into an ice-cold microcentrifuge tube containing 1 ml of anticoagulant buffer and immediately washed twice with anticoagulant buffer. Washed cells were solubilized by adding same volume of 2 × lysis buffer (100 mM HEPES-NaOH, 300 mM NaCl, 3 mM MgCl2, 1 mM EDTA, 20% glycerol, 2% TX-100 (w/v), 1% sodium deoxycholate, 0.2% SDS, pH 7.5) containing Protease inhibitor cocktail (Nacalai tesque, Japan), phosphatase inhibitor cocktail set II (Calbiochem, USA), and 0.2% phenylthiourea. After centrifugation at 17,000 g for 15 min at 4 °C, the supernatant was mixed with the same volume of sample buffer (125 mM Tris–HCl, 10% 2-mercaptoethanol, 4% SDS, 10% sucrose, 0.004% bromophenol blue) and separated by SDS–PAGE (8 or 10%), transferred onto an Immobilon-P PVDF membrane (Millipore, USA). Proteins on the membrane were probed with anti-activated MAP Kinase (diphosphorylated ERK-1&2) mouse monoclonal antibodies (at 1:2,000, M9692, Sigma-Aldrich, USA)38 (link). For reprobing, membranes were washed for 30 min at 50 °C in 62.5 mM Tris–HCl (pH 6.7) containing 100 mM 2-mercaptoethanol and 2% SDS, and they were probed with anti-MAP kinase (ERK-1&2) mouse monoclonal antibodies (at 1:2,000, M5670, Sigma-Aldrich, USA). All positive bands were quantified using ImageJ (NIH).
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10

Antibody Validation for Cellular Assays

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Commercially available primary antibodies (ABs) used in this study for immunoprecipitation (IP), immunofluorescence (IF), proximity ligation assay (PLA), Western blot (WB) and Simple Western capillary system (WES) were: Anti-GFP (abcam, ab6556, IF & WB 1:5000, PLA 1:2000), anti-NFH (abcam, ab72996, 1:2000), anti-Actin (MP, clone C4, 08691001, WB 1:5000), anti-GAPDH (Santa Cruz Biotechnology, sc-32233, WB 1:5000), anti-ERK1/2 (Sigma, M5670, WB 1:30000), anti-β-III tubulin TUJ1 (abcam, ab18207, IF 1:1000, WB: 1:6000), anti-Dynein heavy chain (DYNC1H1, Proteintech , #12345-1-AP, PLA 1:50), antiimportin beta 1 (MBS713065, rabbit, polyclonal, 1:1000).
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