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84 protocols using anti puromycin

1

Antibody Panel for Immunoblot Analysis

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Antibodies used for immunoblots include Rheb (Cell signalling, Cat# 1387, 1:1000), Cre (Cell signalling, Cat# 12830, IHC/IHF - 1:50), Cleaved Caspase 3 (Cell signaling, Cat# 9661, IHC - 1:500), pAkt S473 (Cell signaling, Cat# 4060, 1:1000), pAkt Thr308 (Cell signaling, Cat# 13038, 1:1000), pS6 S240/244 (Cell signaling, Cat# 5364, WB - 1:1000, IHC/IHF – 1:500), Total S6 (Cell signaling, Cat# 2317), p4EBP1 S65 (Cell signaling, Cat# 13443, WB-1:1000, IHC/IHF-1:500), p4EBP1 Thr37/46 (Cell signaling, Cat# 2855, WB-1:1000, IHC/IHF-1:500), 4EBP1 (Cell signaling, Cat# 9644, WB-1:1000), eIF4E (Cell signaling, Cat# 9742, 1:1000), Cyclin D1 (Cell signaling, Cat# 2978, 1:1000), Cyclin D1 (Cell signaling, Cat# 2922, IP-1:50), Cyclin D3 (Cell signaling, Cat# 2936, 1:1000), Actin (Sigma, A5316, 1:5000), PyV mT (clone 762, a gift from Dr. Steven Dilworth, IHC/IHF-1:100), Akt1/2 (Santa Cruz, SC-1619, 1:200), E-Cadherin (BD Bioscience, Cat# 610182, 1:1000), Neu (Dako, A0485, 1:500), Ki67 (Abcam, ab15580, 1:500), Cytokeratin 8/18 (Fitzgerald, 20R-CP004, 1:500), Cytokeratin 14 (BioLegend, PRB-155P, 1:500), and Anti-puromycin (Millipore, Clone 12010 – MABE343, 1:1000). Goat anti-rabbit IRDye 800, Goat anti-mouse IRDye 680, Donkey anti-goat IRDye 800 (Li-COR, 925–32211, 925–68070, 925–68074, 1:10 000)
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2

Measuring Myotube Protein Synthesis

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Myotubes were grown and treated as described previously. To determine the rate of protein synthesis we utilized SUnSET methodology, as described (10 (link), 11 (link)). Briefly, puromycin (Sigma-Aldrich) was administered to the media at a final concentration of 1 μM exactly 30 min before cells were collected in ice-cold homogenizing buffer. Anti-puromycin was purchased from Millipore (Kilsyth, Victoria, Australia) and immunoblotting was used to detect changes in puromycin incorporation as described (9 (link), 10 (link)).
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3

Western Blot Analysis of Mitochondrial Proteins

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NuPAGE™ 4-12% Bis-Tris Protein Gels and NuPAGE® MOPS SDS running buffer was applied for SDS-PAGEs and immunoblot analyses. The following antibodies were used for western blot analyses: Anti-RpL3 (Santa Cruz, sc-86828), anti-RpL7a (Cell Signaling, 2415S), anti-RpS19 (Santa Cruz, sc-100836), anti-RpS6 (Cell Signaling, 2317S), anti-C-IV s.1 (Abcam, ab14705), anti-C-I 30 (Abcam, ab14711), anti-C-I 75 (GeneTex, GTX105270), anti-CORE2 (Abcam, ab14745), anti-TOM20 (Santa Cruz, sc-17764, sc-11415), anti-TOM40 (Santa Cruz, sc-11414), anti-PINK1 (Abcam, ab23707), anti-GST (Sigma, G7781; for mRNP immunoblot), anti-GST (GenScript, A00865; for PLA), anti-myc (Cell Signaling, 2272S), anti-HA (Sigma, 11867423001), anti-GFP (Abcam, ab13970), anti-puromycin (Millipore, MABE343), anti-ABCE1 (a gift from Dr. R Hegde), anti-Pelo (Abcam, ab140615), anti-NOT4 (Abcam, ab72049), anti-dNOT4 (a gift from Dr. E Wahle), anti-dPelo (a gift from Dr. J Han), anti-Ub (Santa Cruz, sc-8017), anti-p-S65-Ub (Millipore, ABS1513-I), anti-K48-Ub (Abcam, ab140601), anti-K63-Ub (Millipore, 05-1308), anti-OPTN (Abcam, ab23666), anti-NDP52 (Abcam, ab68588), anti-P62 (PROGEN, GP62-C), anti-dP62/Ref2P (Abcam, ab-178440), anti-p-TBK1 (Cell Signaling, 5843S), anti-TBK1 (Cell Signaling, 3013S), anti-LC3B (Cell signaling, 2775S).
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4

Puromycin Incorporation Assay in HEK293T

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HEK293T cells were grown in a 6-well plate until 80% confluence and incubated with DMSO, i14G1-10 (20 µM), and i14G-20 (10 µM) for 2 h/3 h, followed by the addition of puromycin (10 µg/mL) for 5 min. The treated cells were lysed using RIPA lysis buffer and lysates and subjected to 10% SDS-PAGE followed by Western blot using anti-puromycin (Millipore).
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5

Compound Library Screening Protocol

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Thapsigargin (Tg), puromycin dihydrochloride, p38 inhibitor (SB203580), and JNK inhibitor (SP600125) were purchased from Sigma (St. Louis, MO, USA). AZD8055 and refametinib were procured from Cayman Chemical (Ann Arbor, MI, USA). The anti-puromycin and anti-glyceraldehyde 3-phosphate dehydrogenase (GAPDH) antibodies were purchased from Millipore (Burlington, MA, USA) and Santa Cruz Biotechnology (Dallas, TX, USA), respectively. The anti-phospho 4E-BP1 (Ser65), anti-4E-BP1, anti-phospho ERK 1/2, anti-ERK 1/2, anti-phospho p38, anti-p38, anti-phospho-JNK, anti-JNK, anti-phospho eIF2α, anti-eIF2α, anti-phospho c-Jun, anti-c-Jun, and horseradish peroxidase-conjugated secondary antibodies were obtained from Cell Signaling Technology (Danvers, MA, USA). Alexa Fluor® 488 AffiniPure Goat Anti-Mouse IgG (Fcγ fragment specific) was supplied by Jackson ImmunoResearch Laboratories (West Grove, PA, USA). The Selleck Anti-Cancer Compound Library consisting of 414 drugs was purchased from the Department of Convergence Medicine, ASAN Medical Center, University of Ulsan College of Medicine (Seoul, Korea).
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6

Immunoblotting Antibody Dilutions

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Anti‐HA: Invitrogen (Cat. No. 26183, 1:10,000 dilution), anti‐GFP: Invitrogen, (Cat. No. A‐6455, 1:1,000 dilution), anti‐RFP: Invitrogen, (Cat. No. MA5‐15257, 1:1,000 dilution), anti‐PABP: Sigma‐Aldrich, (Cat. No. P6246, 1:2,000 dilution), anti‐puromycin: (Millipore, [Cat. No. MABE341, 1:100,000 dilution], anti‐vinculin: Sigma‐Aldrich, [Cat. No. V9264, 1:1,000 dilution], anti‐β‐actin: Santa Cruz, [Cat. No. sc‐47778, 1:500 dilution], anti‐myc: Roche [9E10], 1:300 dilution).
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7

Western Blot Analysis of Stress Response

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OPCs were washed twice with PBS and lysed in ice-cold RIPA buffer (Sigma) containing Halt Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher Scientific, PI78441). Lysates were then centrifuged at 12,000 rpm for 20 min at 4°C. A total 20 µg of protein lysates was separated by 4–12% SDS-PAGE (Bio-Rad, 4561095) and transferred to a nitrocellulose membrane. The following primary antibodies were used: anti-p-eIF2α (Abcam, ab32157, 1:2000), anti-T-eIF2α (Cell Signaling, 9722s, 1:1000), anti-puromycin (Millipore, MABE343, 1:2000), anti-BIP (Cell Signaling, 3177s, 1:1000), anti-GADD34 (Proteintech, 10449–1-AP, 1:500), anti-ATF4 (Santa Cruz, sc-390063, 1:500), anti-CHOP (Thermo Fisher, MAI-250, 1:500), anti-XBP-1-spliced (Cell Signaling, 82914s, 1:1000), and anti-actin (Sigma, A2066, 1:2000). Quantification of Western blot bands were performed by Image Lab Software (Bio-Rad).
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8

Western Blot Analysis of Cellular Signaling

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For whole cell extracts, cells were lysed in EBC buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5% NP-40) supplemented with protease and phosphatase inhibitors. Samples were mixed with Laemmli sample buffer and boiled for 5 min. Protein samples were resolved by SDS-PAGE and transferred to nitrocellulose membranes. Membranes were blocked in PBS-Tween + 5% milk before incubation with primary antibody overnight at 4 °C. Next, membranes were washed in PBS-tween and incubated with HRP Goat Anti-Rabbit or Goat Anti-Mouse IgG Antibody (H + L) for 1 h at room temperature. Lastly, membranes were washed in PBS-tween and visualized by chemiluminescence (Clarity Western ECL substrate, Bio-Rad) using the Bio-Rad Chemidoc imaging system. Antibodies used in this study were: anti-phospho-p38 (Cell Signaling, #9216), anti-p38 (Cell Signaling, #9212), anti-phospho-SAPK/JNK (Cell Signaling Technology, #9255), anti-ZAK (Proteintech, #14945-1-AP), anti-ZAKα (Bethyl #A301-993A), anti-p150 (BD biosciences, #610473), anti-phospho-GCN2 (Abcam, #ab75837), anti-phospho-eIF2α (Cell Signaling, #3398), anti-puromycin (Millipore, #MABE343), anti-EDF1 (Abcam, #ab174651), anti-RPS2 (Bethyl, #A303-794A), anti-RPS10 (Abcam, #ab151550), anti-ZNF598 (Abcam, #ab111698), ASK1 (Thermo Scientific, #702278), α-tubulin (Sigma, #T9026) and anti-HA (Santa Cruz, #sc-7392).
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9

Immunoblot Analysis of Signaling Pathways

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For immunoblot analysis, 1 × 106 neutrophils from wild-type or Ifnlr1−/− mice were stimulated as indicated in the figure legends and were lysed in 100 μl of RIPA buffer supplemented with Protease and phosphatase inhibitor cocktail (Pierce) and diisopropylfluorophosphate (Sigma). Immunoblot analysis was performed using standard techniques. Blots were probed for STAT1 phosphorylated at Tyr701 (clone 14/P-STAT1, BD), STAT2 phosphorylated at Tyr690 (Cat. No. ab53132, Abcam), STAT3 phosphorylated at Tyr705 (Cat. No. 9131, Cell Signaling Technologies), β-actin (clone AC-74, Sigma), Jak2 phosphorylated at Tyr1007 and Tyr1008 (Cat. No. sc-21870, Santa Cruz Biotechnology), Jak2 (clone C20, Santa Cruz Biotechnology), AKT (Cat. No. 9272, Cell Signaling Technology), AKT phosphorylated at Thr308 (clone 244F9, Cell Signaling Technology), AKT phosphorylated at Ser473 (clone 736E11, Cell Signaling Technology), p38 phosphorylated at Thr180 and Tyr182 (clone 36/p38, BD), STAT-1 (Cat. No. 9172, Cell Signaling Technology) and anti-puromycin (clone 12D10, Millipore).
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10

Puromycin Protein Quantification Assay

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48 hours after miRNA transfection LHCN-M2 cells were serum and leucine-starved by incubation in leucine free DMEM. 2 hrs later the medium was replaced with leucine-containing DMEM supplemented with 130nM of IGF-1 (Cambridge Bioscience) and the cells were incubated for 45 minutes, before addition of 100ng/mL puromycin (Sigma) and harvested 30 minutes later and protein extracted. 300 ng of the extracted protein was diluted in 200 µL of 50 mM sodium bicarbonate and incubated in a 96 well plate well at 37°C for 2 hours. The wells were washed (1 X PBS) then blocked with 200 µL PBS containing 5% BSA (w/v) (PBS-BSA) for 30 minutes at RT. The solution was replaced with 100 µL of 100 ng/mL anti-puromycin (Millipore) diluted in PBS-BSA and the samples were incubated for 1 hour at RT. After 2 X PBS washes 100 µL of sheep anti-mouse (GE Healthcare) was added at a 1/10,000 dilution in PBS-BSA. The samples were washed 4 X in PBS before 100 µL of TMB substrate (Sigma) was added and the samples incubated for 15 min. The reaction was stopped with 100 µL of stopping solution (Sigma) and absorbance determined at 450 nm.
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