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12 protocols using complete lysis m kit

1

Protein Extraction and Western Blot Analysis

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Pieces of whole liver were homogenized using a tissue homogenizer (TissueRuptor, Qiagen, Germantown, MD), followed by centrifugation. Protein extraction from cells or whole liver was performed using lysis buffer complemented with protease inhibitor (Complete Lysis M kit, Roche Diagnostics, Indianapolis, IN) and phosphatase inhibitor (Halt Phosphatase Inhibitor Single-Use Cocktail, Thermo Scientific, Waltham, MA). Protein concentration was measured using a Bio-Rad DC kit (Bio-Rad Laboratories, Hercules, CA) and lysates were then subjected to immunoblot analysis. Blots were developed with the ECL Detection System (Amersham, Pharmacia Biotech, Buckinghamshire, England). Densitometry of bands was performed with ImageJ software (rsbweb.nih.gov/ij, NIH, Bethesda, MD). Western blot membranes were incubated with the following primary antibodies: Rabbit anti-β-PDGFR (1:500) and anti-phospho-β-PDGFR (1:500) were obtained from Santa Cruz Biotechnology, Santa Cruz, CA, rabbit anti-CD31 (1:500), rabbit anti-Ki67 (1:2500), rabbit anti-Desmin (1:1000) and rabbit anti-Calnexin (1:3,000) were from Abcam, Cambridge, England). The reactions were detected with the Fujifilm LAS-4000 system (Fujifilm Life Science, Stamford, CT), using a horseradish peroxidase-conjugated secondary antibody (Anti-rabbit IgG, Cell Signaling, Danvers, MA).
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2

Evaluating HER2 Expression in Drug Resistant Cells

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To confirm drug resistance state, cells were seeded and then exposed to different concentrations of trastuzumab. After double wash with cold PBS, the monolayers were scraped into lysis buffer (Complete Lysis-M kit, Roche) and protein isolation was completed according to the instructions manual. The protein concentration was determined using Coomasie Plus Bradford Assay (ThermoScientific) and used to estimate the volume of protein yielding 15 μg, which were boiled in Laemmli buffer and resolved on an 8% SDS-PAGE and transferred onto a PVDF membrane (L-08008-001, Advansta). Primary antibodies were: anti-ErbB2/HER2 (1:1000, ab8054, Abcam) and anti-Beta-actin (1:1000, 634801, Biolegend) was served as a loading control. Mouse secondary antibody (1:10,000, 7076S; Cell Signaling) conjugated with HRP (horseradish peroxidase) was added and kept at room temperature for 60 min. The immunoblot was developed with the WesternBright Sirius Kit (K-12043-D20, Advansta).
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3

Evaluation of ER Stress Markers

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Cells were seeded in T25 flasks at 75×104 cells/flask in growth media and cells were allowed to adhere to the flask overnight in the incubator. The following day cells were treated for 24 h with either: i) PBS; or ii) 1 µM OphA. Cell lysates were prepared using 200 µl of cOmplete Lysis-M kit supplemented with protease and phosphatase inhibitors (Roche Diagnostics) and scraping the cells from the bottom of the flasks. Cell lysates were centrifuged to separate cell debris, and the protein concentration of the supernatant was determined using the BCA assay (Pierce). Protein (10 µg per sample) was mixed with loading buffer, boiled for 4 min and subjected to SDS-PAGE at 120 V followed by a transfer to PVDF membrane for 50 min at 30 V. Membranes were blocked with 5% milk in TBST for 1 h at room temperature and subsequently probed with BiP/GRP78 (1:1,000), PDI (1:1,000), CHOP (1:1,000), cleaved PARP (1:1,000) or β-actin (1:100,000) as a primary antibody overnight at 4°C. Horseradish peroxidase-conjugate secondary antibodies were used and blots were revealed by ECL. Experiments were performed on two separate occasions.
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4

Quantitative Analysis of NF-κB and TNF-α in HepG2 Cells

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HepG2 at a density of 20,000 cells/cm2 treated with 400–1,200 pg/ml of FGF23 were lysed by complete Lysis-M kit (Roche) for cytoplasm and with a second lysis (60 μl of Lysis-M and 10 μl of NaCl 5 M) for the nuclear fractions. The protein lysates were separated on an SDS-PAGE and transferred by electroblotting on a PVDF membrane (Bio-Rad). After blocking, each membrane was incubated with the primary antibody sheep anti-RelA/NFκB 1: 500 (R&D) or anti-TNFα 1:250 (Novus) followed by the HRP-conjugated secondary antibodies 1:200. The products were identified by chemiluminescence (BM Chemiluminescence Western Blotting Kit, Roche). Loading ctrl was conducted with antibodies directed rabbit anti-cofilin 1: 10,000 (SIGMA) and against anti-Histone H3 for Nuclear loading ctrl 1: 1,000 (not shown, Abcam). The images were acquired/analyzed by the Chemidoc XRS instrument and Quantity One software (Bio-Rad).
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5

Quantification of MMP-13 and ANKH Proteins

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The protein levels of MMP-13 and ANKH were determined by Western blot. Total protein was extracted by homogenization with the complete Lysis-M kit (No. 04719956001; Roche) from bovine menisci and quantified by the BAC Protein Assay Kit (Pierce). Equal amounts of protein lysates were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose membranes for immunoblot analysis and stained with specific primary antibodies. The following primary antibodies were used: MMP-13 antibody (H-230, Lot D1113; Santa Cruz Biotechnology) and ANKH antibody (ab90104; Abcam). Fluorescence-labeled secondary antibodies were detected with a fluorescence scanner (Odyssey; LI-COR Biosciences). Band densities were quantified using Image Acquisition and Analysis Software (UVP). Parallel gels were prepared for Coomassie Blue staining to confirm equal loading of the samples as described.43 (link) Equal amounts of protein were electrophoresed in 10% SDS-PAGE, and the gel was prefixed in 50% MeOH, 10% HoAC, and 40% H2O for 30 minutes and then stained with 0.25% Coomassie Brilliant Blue R-250 (Bio-Rad Laboratories) in the above solution for 4 hours. The gel was destained in 5% MeOH, 7.5% HoAC, and 87.5% H2O until the background was clear. The destained gel was stored in 7% HoAC, and a photograph was taken using a Canon camera (SD-1000; Canon Inc).
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6

Quantitative Western Blot Analysis

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Cells in culture were lysed using Complete Lysis-M kit (Roche). The protein concentrations of the lysates were quantified using Coomassie Plus Protein Assay Reagent (Thermo Scientific). 10 ug of protein for each sample were loaded on to 8% SDS-PAGE gel. Separated proteins were transferred to a PVDF membrane (L-08008-001, Advansta) in wet transfer buffer. Membranes were blocked with 5% milk in TBST (0.5%) for 1 hour at room temperature before incubation at +4°C overnight with the following antibodies: HER2 (1:1000, ab8054, Abcam), total AKT (1:1000, sc8312, SantaCruz), phospho-AKT (Ser 473, 1:1000, sc-7985-R, SantaCruz), total ERK2 (1:1000, sc-154, SantaCruz), phosho-ERK 1/2 (Thr 202 / Tyr 204, 1:1000, sc-81492, SantaCruz) and beta-actin (1:1000, 634801, Biolegend) in 3% milk powder-TBST. After incubation with HRP-conjugated secondary antibodies, the protein bands were detected using WesternBright Sirius Kit (K-12043-D20, Advansta).
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7

Lung Protein Expression Analysis

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Whole tissue lysates were prepared from flash-frozen lung tissue using the cOmplete Lysis-M kit (Roche Diagnostics, Indianapolis, IN) and protein was separated on a 10% acrylamide gel. Western blot analysis was performed with Rabbit polyclonal antibodies against MMP12 (ab52897, Abcam; 1:1,000), sheep polyclonal antibodies against neutrophil elastase (61-86-20, Invitrogen, Camarille, CA; 1:1,000) or rabbit polyclonal against β-actin (A2066, Sigma-Aldrich; 1:2,000).
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8

Quantifying Pyrophosphate and Phosphate Levels in Meniscus Lysates

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The menisci of the right (ACLT) and left (control) knees were lysed using the complete Lysis-M kit (#0471 9956001; Roche) (n = 3). The concentrations of PPi and Pi in solution were detected by enzyme-linked immunosorbent assay (ELISA) using the EnzChek Pyrophosphate Assay Kit (E-6645; Molecular Probes) and EnzChek Phosphate Assay Kit (E-6646; Molecular Probes), respectively, following manufacturer instructions using 60-μL lysed samples. The reaction mixtures were incubated for 30 minutes at 22°C, and then the absorbance was read at 360 nm.
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9

Western Blot Analysis of Cellular Signaling

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Untreated as well as transfected whole cell lysates were prepared using the cOmplete Lysis-M kit (Roche Applied Science, Indianapolis, IN). Protein samples were prepared by combining lysates with NuPAGE Sample Reducing Agent, NuPAGE LDS Sample Buffer, and nuclease-free water (Life Technologies) and then boiling for 5 minutes at 100°C. Samples were loaded onto NuPAGE 4-12% Bis Tris Gels (Life Technologies), separated by SDS-PAGE, and then transferred to PVDF membranes. Proteins were blocked in 5% non-fat milk and incubated with the appropriate antibody in 5% BSA (Sigma-Aldrich). The following antibodies were used for Western blot analyses: AKT (#9272), pAKT Thr308 (#4056), pAKT Ser473 (#4058), CASP7 (#9492), Fox01 (#2880), pFox01 Ser256 (#9461), GSK-3β (#9315), pGSK-3β Ser9 (#9336), INNPL1 (#2839), p70 S6 Kinase (#2708), PDK1 (#5662), pPDK1 Ser241 (#3438), PI3K p85 (#4292), and GAPDH (#2118) [Cell Signaling, Danvers MA]; and pGSK-3β Tyr216 (#75745) [Abcam Inc., Cambridge, MA]. Protein bands were visualized using Pierce ECL Western Blotting Substrate (Thermo Fisher Scientific, Rockford, IL).
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10

Dbr1-FLAG Immunoprecipitation and Mass Spectrometry

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10-cm dishes of HEK293T cells were transfected with a Dbr1-FLAG plasmid37 (link). 2 days post-transfection, cells were harvested with Roche Complete M lysis kit, EDTA free according to the manufacturer’ protocol (Roche, 04719964001). Three dishes of Dbr1-FLAG transfected cells, and 3 dishes on un-transfected HEK293T cells were harvested. For each dish, 1 ml of 1 mg/ml lysate with used for immunoprecipitation with anti-FLAG M2 magnetic beads (Sigma, M8823) following the manufacturer’s protocol. Samples were eluted with 50 ul of 2x SDS-PAGE loading dye and submitted for mass-spectrometry.
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