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19 protocols using protein marker

1

Adipogenesis Pathway Characterization

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The culture medium Dulbecco's modified Eagle's medium (DMEM) used in all the experiments was purchased from Lonza. The triacylglycerol assay kit was purchased from Abnova. NBD-ceramide (NBD-N-hexanoyl-D-erythro-sphingosine) was from Cayman Chemicals. Dexamethasone, rosiglitazone, insulin, 3-isobutyl-1-methylxanthine (IBMX), and the Oil Red O dye were obtained from Sigma-Aldrich. Nitrocellulose membranes, protein markers, and BCA assay reagents were purchased from Bio-Rad. Fetal bovine serum (FBS) and newborn calf serum (NCS) were from GIBCO. The ELISA kit for determination of leptin was purchased from Peprotech. The PPARγ antibody was supplied by Cell Signaling. The GAPDH antibody, nontargeting (negative) siRNA, and ceramide kinase (CerK) siRNA were purchased from Santa Cruz Biotechnology. The CerK antibody was from Calbiochem or Abgent. The rest of chemicals and reagents used in this work were of the highest grade available.
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2

Biochemical Assays for DNA Repair Enzymes

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Synthetic oligonucleotides were obtained from Laboratory of Biomedicinal Chemistry (ICBFM SB RAS, Russia). [γ-32P] ATP (3000 Ci/mmol), [α-32P] ATP (3000 Ci/mmol) and [α-32P] dCTP (3000 Ci/mmol) were from Laboratory of Biotechnology (ICBFM SB RAS, Russia). T4 polynucleotide kinase, E. coli uracil DNA glycosylase, T4 DNA ligase were from Biosan, Russia. The plasmids containing cDNA of human apurinic/apyrimidinic endonuclease 1 (APE1) and rat DNA polymerase β (Pol β) were a kind gift of Dr. S.H. Wilson (National Institute of Environmental Health Sciences, NIH, NC, USA). Recombinant APE1 and Pol β were purified as described previously [74 (link),75 (link)]. FAP-dCTP was synthesized as described [44 (link)]. Proteinase K and benzonase were from Merck and Novagen, respectively. Protein markers were from Bio-Rad. Cell proliferation & toxicity assay (EZ4U Assay) was from Biomedica.
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3

SDS-PAGE Protein Separation Protocol

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SDS/PAGE was performed as described by Laemmli 67 using 10% polyacrylamide gels. Protein markers, consisting of a mixture of recombinant proteins (10–250 kDa), were purchased from Bio‐Rad (Tokyo, Japan).
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4

Western Blot Analysis of Lung Tissues

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Lung tissues were lysed in RIPA buffer (1% Triton X-100, 0.5% sodium deoxycholate, 0.2% SDS, 150 mM NaCl, 10 mM Hepes, pH 7.3, 2 mM EDTA, and protease inhibitor mixture; Pierce), as we previously described 12 (link). After blocking, membranes were probed overnight at 4°C with the primary antibodies as follows: APJ (SC-33823; Santa Crutz, USA), Bax (14796; CST, USA), Caspase 3 (9662; CST, USA), Cleaved caspase 3 (9661; CST, USA), ɑ-SMA (14968; CST, USA), CD31 (3528; CST, USA), and GAPDH (2118; CST, USA). HRP-conjugated anti-rabbit or anti-mouse (CST) was used to detect the primary antibodies. After washing, the protein bands were visualized using an enhanced chemiluminescence (Bio-Rad). The relative expression of the proteins was quantified using densitometric scanning and analyzed by the Imaging J System and expressed as percent of controls. Molecular mass was determined relative to protein markers (BioRad).
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5

Adipocyte Differentiation Assay Protocol

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Insulin, rosiglitazone, dexamethasone, HEPES, NaHCO3, Oil Red O, sodium deoxycholate, and phenylmethylsulfonyl fluoride were obtained from Sigma-Aldrich (St Louis, MO, USA). SDS, Tween 20, and isopropanol were purchased from GENEray (Shanghai, China). Paraformaldehyde was obtained from TCI (Tokyo, Japan). All antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Western blotting loading buffer, Bio-Rad protein assay reagents, and protein markers were obtained from Bio-Rad (Hercules, CA, USA). Triglyceride (TG) and glucose detection kits were purchased from Asan Pharmaceutical (Seoul, Korea).
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6

Protein Kinase Inhibitors Analysis

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Protein kinase inhibitors staurosporine, H-89, chelerythrine, Gö6983 and tyrphostin 23 were purchased from the Sigma-Aldrich Co. ReadyStrip IPG strips, protein markers and polyvinylidene difluoride (PVDF) membranes were from Bio-Rad laboratories. Anti-phosphotyrosine, anti-phosphoserine, anti-phosphothreonine and anti-PKC polyclonal antibodies produced in rabbit were from Abcam. Phospho-(Ser/Thr) PKA substrate, phospho-(Ser) PKC substrate and PKA C-α polyclonal antibodies produced in rabbit and HRP-conjugated goat antirabbit IgG were purchased from Cell Signaling Technology (Biotech A.S., Prague, Czech Republic).
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7

Evaluation of Apoptosis Induction in Cell Lines

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RPMI-1640 medium, fetal bovine serum (FBS), penicillin-streptomycin, and Dulbecco's Phosphate Buffered Saline (DPBS) were purchased from Gibco-BRL (Burlington, Ont, Canada). 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), dimethyl sulfoxide (DMSO), Hoechst 33342, ribonuclease A (RNase A), and propidium iodide (PI) were obtained from Sigma (St. Louis, MO, USA). DNA ladder size markers were purchased from Invitrogen (Carlsbad, CA, USA). Antibodies against Bcl-2, Bax, caspases 3 and 9, cleaved PARP, and β-actin were purchased from Cell Signaling Technology (Bedford, Massachusetts, USA). Protein marker was purchased from Bio-Rad (Richmond, CA, USA). Caspase 3 activity assay kit was purchased from Promega (San Luis Obispo, CA, USA). All other chemicals and reagents used herein were of analytical grade.
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8

Protein Extraction and Immunoblotting

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Referring to the previous description (32 (link)), protein extraction and immunoblotting were performed. The antibodies directed against the following proteins, including PI3K, p-PI3K, AKT, p-AKT, and β-actin were used, and their directions are shown in Table 1. HRP-conjugated secondary antibodies (1:5,000, GeneTex, Irvine, CA, USA) were also used. Other materials consisted of electrophoresis and membrane transfer device (Bio-Rad), RIPA lysate (Beyotime), protease inhibitor (cocktail) (Roche), ECL chemiluminescence substrate Kit (Biosharp, Hefei, China), defatted milk powder (Wondersun, Harbin, China), protein marker (Bio-Rad), BCA kit (Beyotime), and SDS-PAGE gel rapid preparation kit (Beyotime). Blotting was captured by Molecular Imager ChemiDocTM XSR+ Gel Imaging System (Bio-Rad) and analyzed using ImageJ software (NIH). In semiquantitative analysis of the target protein, each sample was normalized to β-actin.
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9

Protein Purification and Characterization

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The detailed procedures of protein purification are described in the Supplementary Methods. After purification of nickel column, the 14-3-3 ζ protein was digested overnight at 4 °C with TEV protease at a ratio of 1:30 (protease : protein) [24 (link)] to remove the label. Under denaturing conditions, the molecular weight was estimated using a protein marker (Bio-Rad, California, USA) as a reference protein, and protein purity was evaluated by sodium lauryl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on a 15% polyacrylamide gel (Supplementary Figure 2). The concentration of 14-3-3 ζ protein was then detected at the absorbance of 280 nm by using a molar absorptivity constant calculated using the ExPASy/ProtParam tool (https://web.expasy.org/protparam/) [25 (link)].
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10

Edible Birds' Nest Protein Characterization

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Dry edible birds’ nest samples (Aerodramus fuciphagus) originated from Indonesia and were kindly donated by Xiamen Yanzhiwu Sinong Food Co., Ltd. (Xiamen, China). Edible birds’ nest samples with a higher content of protein (66.18 ± 0.76%) were milled by a high-speed universal crusher (SS-1022, Shengshun, Jinhua, China) and then passed through a 120-mesh sieve. A sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) kit and protein marker were obtained from Bio-Rad (Hercules, CA, USA). 1-anilinonaphthalene-8-sulphonate (ANS) was obtained from Sigma-Aldrich Co., Ltd. (St. Louis, MO, USA).
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