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10 protocols using glycolysis antibody sampler kit

1

Protein Extraction and Immunoblotting

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Cell lysates were prepared with lysis buffer containing 20 mM Tris (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 2.5 mM sodium pyrophosphate, 1 mM β-glycerophosphate, 1 mM Na3VO4, 1 μg/ml leupeptin. 1 mM PMSF was added immediately prior to use. The protein concentration was measured by DC protein assay (Bio-Rad). The primary antibodies and dilutions were used as follow: glycolysis antibody sampler kits (#8337&12866, Cell Signalling) used at 1:1000; the OXPHOS human WB Antibody cocktail, anti-CS and IDH2 used at 1:1000 (Abcam); anti-HSP60 and SUCLA2 (Santa Cruz); anti phospho AMPK T172 and AMPK, anti phospho ribosomal S6 Ser235/236 and S6; anti phospho mTOR Ser2481 and mTOR used at 1:1000 (Cell Signaling). Generally, 20 μg of protein lysate were loaded on SDS-PAGE gel. Immunoblotting quantification was carried out on an Odyssey Imager (Licor).
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2

Neuronal Nuclear Extract Preparation

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Cell lysates were prepared with lysis buffer containing 20 mM Tris (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 2.5 mM sodium pyrophosphate, 1 mM β-glycerophosphate, 1 mM Na3VO4, 1 μg/ml leupeptin. 1 mM PMSF was added immediately prior to use. The protein concentration was measured by DC protein assay (Bio-Rad, Irvine, CA). Quick neuron nuclear extract preparation: the cells were rinsed with PBS once, and plates placed on ice and 1 ml of ice cold Buffer A (25 mM Hepes pH 7.0, 25 mM KCl, 0.05 mM EDTA, 5 mM MgCl2, 10% glycerol, 0.1% NP-40, 1 mM DTT) added. The plate was scraped and cells were transferred into an Eppendorf tube, which was centrifuged and rinsed once with Buffer A (no NP-40). The pellet was resuspended in PBS, and 2x SDS PAGE sample buffer added, prior to boiling for 10 min at 95°C. The following primary antibodies and dilutions were used: antibodies against the major glycolysis enzymes were from Cell Signaling sold as glycolysis antibody sampler kits (#8337&12866); all were used at 1:1000; Rabbit anti-TFAM (Cell Signaling) used at 1:1000; Rabbit anti-CS, IDH2, PGC-1α and ATP5O (Abcam, Cambridge, United Kingdom) used at 1:1000, and mouse anti-Sucla2 and goat anti-Hsp60 (Santa Cruz Biotechnology) used at 1:1000. Immunoblotting results were analyzed by Odyssey Imager (Licor, Lincoln, NE) scanning.
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3

Comprehensive Glycolysis Pathway Analysis

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A Cell Counting Kit-8 (CCK-8, Cat# CK04) was purchased from Dojindo (Kumamoto, Japan). Pooled antisense oligonucleotides (i.e., siRNAs) against human OVOL2, P65, and GLUT1 were purchased from GenePharma (Shanghai, China). Antibodies against OVOL2 (Cat# ab101580) and P65 (Cat# ab16502) were purchased from Abcam (Cambridge, MA, USA). The following antibodies were used: Glycolysis Antibody Sampler Kits (Cell Signaling Technology; Cat# 12866 and Cat# 8337), anti-GLUT1, anti-GLUT2, anti-GLUT3, anti-GLUT4, anti-PGK1, anti-GCK, anti-PDP2, anti-DLD, anti-PCK1, anti-SDHA, anti-G6PD (all from Abcam; Cat# ab115730, ab234440, ab191071, ab188317, ab38007, ab184169, ab99170, ab133551, ab28455, ab14715, and ab210702, respectively), anti-GAPDH anti-Lamin B, anti-actin and anti-Calnexin (all from Cell Signaling Technology; Cat# 8884, 13435, 3700 and 2433, respectively).
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4

Protein Expression Analysis of Mitophagy, Dynamics, and Glycolysis

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Protein was extracted from cultivated cells with RIPA buffer, separated by SDS-PAGE, and then transferred to PVDF membranes. Then antibodies were applied per the manufacturer’s instructions (Mitophagy Antibody Sampler Kit #43110, Mitochondrial Dynamics Antibody Sampler Kit #48799, and Glycolysis Antibody Sampler Kit #8337 Cell Signaling Technology, Danvers, MA, USA) or antibodies against IL-17RB (ProteoTech, Attendorn, Germany, 1:1000), Actin (Abcam, Cambridge, UK, 1:5000) were used to probe proteins. In addition, HRP-conjugated sheep anti-mouse/Rabbit IgG antibodies (1:5000, Cell Signaling Technology, Danvers, MA, USA) were applied to visualize protein expressions with the Pierce ECL Western blotting substrate (Thermo Fisher Scientific, Waltham, MA, USA).
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5

Cell Surface Protein Isolation and Analysis

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This was achieved using a Pierce-Thermo Cell Surface Protein Isolation Kit Pierce (#89881) in which cell surface proteins were labelled with a cleavable biotin (Sulfo-NHS-SS-Biotin) in intact live cells for 1 h at 4 °C. Biotin-labelled protein was extracted using NeutrAvidin conjugated agarose beads, eluted using dithiothreitol and denatured at 95 °C for 5 min in SDS sample buffer, prior to separating using SDS-PAGE and western blotting for glycolytic enzymes and PMCA. Dithiothreitol precluded protein quantification from biotinylated fractions. Primary antibodies used include non-specific PMCA (PMCA NS (5F10)), PMCA1 and PMCA4 (JA9) (Thermo Pierce) and the Glycolysis Antibody Sampler Kit (Cell Signaling Technology, Kit 8337).
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6

Glycolytic Enzyme Expression Analysis

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The total protein was extracted using RIPA buffer (Thermo Fisher Scientific) added to the cocktail of proteinase inhibitor and phosphorylase inhibitor. The Western blot procedure was performed as has been done previously 15 (link). The primary antibodies: Phosphofructokinase (PFK), Platelet-type phosphofructokinase (PFKP), GAPDH, the M1 and M2 isoform of Pyruvate kinase (PKM1 and PKM2) and LDHA were from Glycolysis Antibody Sampler Kit #8337 (cell signaling technology, CST). For secondary antibodies either anti-rabbit (#14708) or anti-mouse (#14709) IgG conjugated with horseradish peroxidase (CST) were used. Western Lightning ECL (Bio-Red) reagents were used for fluorescence production and a ChemiDoc™ Imaging System (Bio-Rad Laboratories, US) was used to visualize the protein detected.
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7

Western Blot Analysis of Signaling Pathways

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Cells or xenografts were homogenized in RIPA buffer as described (32 (link)). Samples containing 30 μg protein were separated by SDS-PAGE and blotted onto PVDF membranes. The anti-phosphorylated ERK1/2 (1:1,000), anti-phosphorylated AKT (1:1,000), anti-ERK1/2 (1:1,000), anti-AKT (1:1,000), anti-phosphorylated FRS2α (1:1,000), and anti-HA (1:1,000) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Anti-pLDHA (1:1,000), anti-LDHB (1:1,000), and anti-LDHA 1:1,000) antibodies and the Glycolysis Antibody Sampler Kit containing antibodies against HK1, PFKP, PFKP2, PFKP3, aldolase, PGAM, PKM1/2, and pyruvate dehydrogenase were purchased from Cell Signaling Technology (Danvers, MA). The anti-phosphotyrosine 4G10 (1:1,000), anti-TET1 (1:1,000), and anti-Flag (1:1,000) antibodies were purchased from Millipore Sigma (Danvers, MA). The specifically bound antibodies were visualized using the ECL-Plus chemiluminescent reagents. The films were scanned with a densitometer for quantitation.
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8

Metabolic Modulation in Cancer Cells

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CPI-613 was obtained from Selleckchem (Houston, TX). 2′,7′-dichlorofluorescin diacetate (DCFH-DA), chloroquine (CQ), N-acetylcysteine (NAC), Compound C, simvastatin, and 5-(tetradecyloxy)-2-furoic acid (TOFA) were purchased from Sigma-Aldrich (St Louis, MO). Fatty acid and lipid metabolism antibody sampler kit and glycolysis antibody sampler kit were purchased from Cell Signaling Technology (Beverly, MA). Fatty acid and lipid metabolism antibody sampler kit includes antibodies against Acetyl-CoA Carboxylase (ACC), p-Acetyl-CoA Carboxylase (p-ACC) (Ser79), AceCS1, ACSL1, Lipin 1, ATP-Citrate Lyase, p-ATP-Citrate Lyase, Fatty Acid Synthase (FAS). glycolysis antibody sampler kit includes GAPDH, PDH, HKI, HKII, LDHA, PKM2, PKM1/2, and PFKP. Antibodies against c-Caspase 3, PARP, p-mTOR (Ser2448), mTOR, p62, LC3B, p-AMPKα (Thr172), AMPKα, p-ULK1, ULK1, Bax and Bcl-2 were purchased from Cell Signaling. Apoptotic rate was determined using Annexin V-FITC Apoptosis Detection Kit (BD Biosciences, San Jose, CA). All flow cytometry data was analyzed using FlowJo software (Tree Star, Ashland, OR). Cell viability was determined by MTT assay, crystal violet staining, and alamarBlue Cell Viability Reagent (Thermo Fisher Scientific, Waltham, MA). Western blot, plasmid transfection and lentiviral infection were carried out as we previously described [15 (link)–17 ].
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9

Immunoblotting and Immunofluorescence Assay

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PMA, LPS, IFN-γ, IL-4, IL-10, and SP600125 were purchased from Sigma-Aldrich. 2-Deoxy-D-glucose (2-DG), heptelidic acid (HA), oligomycin (Omy), LW6, and YC-1 were from MCE (United States). Meloxicam was from TCI (Japan). Immunofluorescence blocking buffer (#12411), and Alexa Fluor 488 goat anti-rabbit (#4412; RRID: AB_1904025) and Alexa Fluor 594 goat anti-mouse (#8890; RRID: AB_2714182) secondary antibodies were purchased from Cell Signaling Technology. Antibodies against β-actin (#3700; RRID: AB_2242334), phospho-SAPK/JNK (#4668; RRID: AB_823588), SAPK/JNK (#9252; RRID: AB_2250373), phospho-p44/42 MAPK (Erk1/2) (#4370; RRID: AB_2315112), p44/42 MAPK (Erk1/2) (#4695; RRID: AB_390779), phospho-p38 MAPK (#4511; RRID: AB_2139682), p38 MAPK (#8690; RRID: AB_10999090), COX-2 (#12282; RRID: AB_2571729), and HIF-1α (#36169; RRID: AB_2799095) and Glycolysis Antibody Sampler Kit (#8337; RRID: AB_10897509) were obtained from Cell Signaling Technology. The secondary antibodies of IRDye 680RD donkey anti-mouse IgG and IRDye 800CW donkey anti-rabbit IgG were purchased from LI-COR.
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10

Molecular Characterization of p53 Mutants

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The His-tagged p53 was generated into the pET30a vector, and His-p53-S46A was mutant based on His-p53. The no-tag plasmid pcDNA3.1-p53, pcDNA3.1-p53-S33A, pcDNA3.1-p53-S46A, pcDNA3.1-p53-T81A, pcDNA3.1-p53-4M were obtained from Giannino Del Sal. p53-K24R was mutant based on pcDNA3.1-p53. The Flag-pcDNA-p53, Flag-pcDNA-p53-1-300, Flag-pcDNA-p53-101-300, Flag-pcDNA-p53-101-393 were obtained from Mu-shui Dai. pcDNA-p53-8KR was obtained from Wei Gu. The following antibodies were commercially purchased: Anti-Flag (Sigma-Aldrich, St. Louis, MO, USA), anti-p53 (DO-1, FL-393 Santa Cruz Biotechnology), pan anti-crotonyl (ptm-501, PTM Biolabs), anti-GAPDH (#5174, Cell Signaling Technology), anti-β-actin (C4, Santa Cruz Biotechnology), anti-PFKP, anti-PKM2, anti-HK2, anti-LDHA (#8337, Glycolysis Antibody Sampler Kit, Cell signaling Technology).
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