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19 protocols using ripa strong lysis buffer

1

Zebrafish Protein Extraction and Purification

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At 55 hpf, approximately 200 zebrafish larvae pooled from 5 independent MO injection experiments were collected and washed with PBS buffer. 500 µl RIPA lysis buffer (Strong) (Beyotime Institute of Biotechnology, Nanjing, China) containing 1× protease inhibitor cocktail (Thermo Scientific, Waltham, MA, USA) was added to each sample, and then the samples were disrupted by intermittent sonic oscillation (5 s on, 5 s off) for 5 min on ice. Next, the lysates were incubated on a shaker for 30 min at 4 °C. Cellular debris were removed by centrifugation at 12,000 × g for 1 h at 4 °C. Four-fold of ice-cold acetone was added into the supernatant. The supernatant was acetone-precipitated at −20 °C overnight and then centrifuged at 12,000 × g for 30 min at 4 °C. Protein concentrations were determined using the BCA protein assay kit (Thermo Scientific). Part of the protein samples were aliquoted and stored in −80 °C for the western blot (WB) assay. The remaining samples were subjected to trypsin digestion according to Xiong et al.44 (link). After digestion, a Strata X-C18 SPE column (Phenomenex, Torrance, CA, USA) was used for desalting.
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2

Western Blot Analysis of P53 and β-actin

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Western blot was performed strictly according to previously described procedures (Chen et al., 2022 (link)). Briefly, cells were washed with ice-cold PBS and soluble proteins were extracted with RIPA Lysis Buffer (Strong) (Beyotime Biotech, Shanghai, China) according to the manufacturer’s protocol. The protein concentration of each sample was determined by a BCA Kit (Beyotime Biotech, Shanghai, China). An equal amount of protein was separated by SDS-PAGE and transferred onto a nitrocellulose membrane (Millipore, Billerica, MA). The membrane was then blocked with 5% non-fat milk for 2 h at room temperature and incubated with primary antibodies overnight at 4°C. Antibodies against P53 (Santa Cruz Biotechnology, Santa Cruz, USA) and β-actin (Proteintech, Wuhan, China) were used. Signals were visualized using infrared imaging systems (Odyssey CLX, LiCor Biosciences, Lincoln, NE).
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3

Protein Extraction and Western Blot Analysis

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Proteins were extracted from the roots of the sample using the RIPA lysis buffer (strong) (Beyotime, China). For Western blot analysis, proteins were electroblotted from 10% acrylamide gel to nitrocellulose membrane (Immobilon‐P, MILLIPORE Corporation, Bedford, MA, USA) after the separation of SDS‐PAGE. Antibodies used in Western blot were as follows: anti‐GFP antibody (M20004, Mouse mAb, Abmart, Shanghai, China), 1 : 1000 for Western blot; anti‐ACTIN antibody (M20009, Mouse mAb, Abmart, Shanghai, China), 1 : 1000 for Western blot and goat anti‐mouse lgG‐HRP (M21001, Abmart, Shanghai, China), 1 : 5000 for Western blot. Image Quant LAS 4000 (GE, USA), as the CCD camera system, was used for the band intensity quantification with Super Signal West Femto Trial Kit (Thermo, Rockford, IL, USA).
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4

Investigating Protein Signaling in Cell Stress

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Cells (3.0 × 107) were treated with 0.5 mM NAC, BA (12.5, 25, 50 or 100 μg/ml) and an equal volume of RPMI-1640 medium for 2 h. HPS (3.0 × 107 CFU/ml) was added and the protein was extracted after 6 h using RIPA Lysis Buffer Strong (P0013, Beyotime Biotechnology, Shanghai, China). The protein concentration was determined by BCA protein assay kit (P0012, Beyotime Biotechnology). The proteins were separated by 10% SDS-PAGE and transferred onto a PVDF membrane (60 mA, 1 h). The PVDF membrane was blocked with 5% skimmed milk at 20 °C for 3 h, then incubated with the primary antibody (containing 5% BSA TBS-T solution, 1:1000 dilution, Anti β-actin, cleaved caspase-3, JNK, p-JNK, p38, p-p38, ERK, p-ERK, PKC-α and p-PKC-δ, Cell Signaling Technology, MA, USA; and p-PKC-α and PKC-δ, Sigma, USA) overnight at 4 °C and the secondary antibody (containing 5% skimmed milk TBS-T solution, 1:2000 dilution; Cell Signaling Technology) at room temperature for 3 h. Afterwards, the membrane was visualized by ECL solution (Thermo Pierce ECL, USA) using a ChemiDoc MP Imaging System (Bio-Rad, Hercules, CA, USA). The β-actin was used as an inner loading control. Gray value was analyzed and the relative expression level of protein was obtained.
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5

Proteomic Analysis of Ventral Midbrain in MAP2K5 Mutant Mice

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Map2k5+/– mutant mice and WT littermates (female, aged 21 weeks, n = 4 per group) were perfused with PBS and sacrificed. Brains were then dissected quickly within 10 min and snap frozen in liquid nitrogen. Proteins were prepared from the ventral midbrain (Yun et al., 2018 (link)) including nigrostriatal dopaminergic neurons. Cytoplasmic proteins were extracted by RIPA Lysis Buffer (Strong) (Beyotime Biotechnology, Shanghai, China) supplemented with Complete Protease Inhibitor Cocktail (10×) and PhosSTOPTM Cocktail (10×) (Roche Ltd., Basel, Switzerland). Western blots were performed using sodium dodecyl sulfate polyacrylamide gel electrophoresis and nitrocellulose membranes. Primary antibodies included anti-tyrosine hydroxylase Ab (1:1,000, MAB318, Millipore Co., Massachusetts, United States), Erk5 Antibody (1:1,000, #3372, CST Ltd., Boston, United States), Phospho-Erk5 (1:1,000, Thr218/Tyr220), Antibody (1:1,000, #3371, CST), MAP2K5 (Concordet and Haeussler, 2018 (link)). Antibody (1:200, sc-135986, Santa Cruz Biotechnology, Inc., Northern California, United States), and GAPDH (D16H11) XP® Rabbit mAb (1:1,000, #5174, CST). Signals were detected with an ECL agent (Millipore). Blotting images were acquired and quantitatively analyzed by Image Lab Software (Bio-Rad, CA, United States).
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6

Quantitative Analysis of Protein Expression

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Proteins were extracted using RIPA lysis buffer (strong) (Beyotime, China) from 2-week-old seedlings grown hydroponically on medium containing different N concentrations of 0.02 mM, 0.2 mM, and 2 mM KNO3 without salt as a control or with 100 mM NaCl. For western blot analysis, proteins were electroblotted from a 10% acrylamide gel to a nitrocellulose membrane (Immobilon-P, Millipore, Bedford, MA, USA) after SDS‒PAGE separation. The antibodies used in western blotting were as follows: anti-GFP antibody (M20004, Mouse mAb, Abmart, Shanghai, China), 1:1000; anti-ACTIN antibody (M20009, Mouse mAb, Abmart, Shanghai, China), 1:1000; and goat anti-mouse lgG-HRP (M21001, Abmart, Shanghai, China), 1:5000. An Image Quant LAS 4000 (GE, USA) CCD camera system was used to quantify band intensity with the Super Signal West Femto Trial Kit (Thermo, Rockford, IL, USA).
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7

Endoplasmic Reticulum Stress Response in HUVECs

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HUVECs were purchased from Shanghai Bogoo Biotechnology (Bogoo, SHH, China). Fetal bovine serum (FBS), 1640 medium, and trypsin (containing EDTA) were purchased from the Hyclone Company (Logan, UT, USA). Probucol, tetrazolium (MTT), and dimethyl sulfoxide (DMSO) were purchased from Sigma (Sigma-Aldrich, Oakville, CA, USA). LDH assay kits were obtained from Pierce Biotechnology (USA). RIPA lysis buffer strong, BCA protein assay kit, antibody dilution, and SDS-PAGE Sample Loading Buffer (5X) were purchased from Beyotime Biotechnology (Beyotime, SHH, China). Rabbit anti-GRP78 monoclonal antibody, rabbit anti-XBP-1 monoclonal antibody, and mouse anti-CHOP/GADD153 monoclonal antibodies were purchased from CST (Beverly, MA, USA). Horseradish peroxidase (HRP)-conjugated goat anti-mouse antibody and HRP-conjugated goat anti-rabbit antibody were supplied by ZSGB-BIO (Beijing, China). Polyvinyl difluoride membrane (PVDF; 0.45 µm) was purchased from Millipore (Billerica, MA, USA).
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8

Protein Expression Analysis of BC Tissues

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A total of 30 pairs of primary BC fresh tissues and cells were lysed with radioimmunoprecipitation assay (RIPA) lysis buffer (strong; Beyotime, China) in the presence of protease inhibitors (Roche). Equal amounts of cellular proteins were loaded into each well and resolved using 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels. The samples were heated for 5 min at 95°C. Polyvinylidene fluoride membrane blotting was subsequently performed under standard conditions. For immunoblotting, the following primary antibodies were used against pEGFR (ab40815; Abcam, US), EHD1 (ab51504; Abcam, Hong Kong), RAB11FIP3 (ZM-0442; ZSGB-BIO, China), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH; Sigma). The primary antibody solution was diluted 1:1000 and incubated with the membrane overnight at 4°C. The primary antibody against GAPDH (Sigma) solution was diluted 1:5000 and incubated with the membrane overnight at 4°C. The membrane was subsequently washed three times for 10 min with a mixture of tris-buffered saline and Tween 20 (TBS-T) prior to adding a 1:5000 dilution of the secondary antibody, which was diluted in the TBS-T solution at room temperature. The membrane was then incubated on a swing bed for 1 h prior to three 10-min washes with TBS-T.
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9

Protein Extraction and Western Blotting

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Cell samples were collected and quickly incubated with cold RIPA‐strong lysis buffer (Beyotime Biotechnology) which contains 1% protease inhibitor cocktail (Cwbiotech) and 1% phosphatase inhibitor (Cwbiotech) over 30 min. The lysis sample was then centrifuged at 12,500 rpm at 4°C for 30 min. The supernatant was collected, and a BCA (Thermo Fisher Scientific) assay was used for protein quantitation. A total of 30 μg of protein sample was added to each lane of a sodium dodecyl sulphate–polyacrylamide gel. Proteins were transferred to a polyvinylidene fluoride membrane (0.2 μm; Millipore) after electrophoresis. The membrane was then blocked with 5% skimmed milk at room temperature for 1 h and incubated with the indicated primary antibodies overnight at 4°C. All primary antibodies used in this research were diluted in 1:1000. Later, the membranes were washed with PBST buffer and incubated with secondary antibody for 2 h at room temperature. The secondary antibodies were diluted in 1:10,000. Finally, the targeted protein band was illuminated with ECL Western Blotting Substrate (Millipore).
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10

Western Blot Analysis of CDK19 Protein

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Cells were lysed with RIPA strong lysis buffer (Beyotime, China) supplemented with the protease inhibitors, 1% PMSF (Roche, Mannheim, Germany), and PIC (Roche, Switzerland). After centrifugation for 15 min, protein concentration in the supernatant was measured using a Pierce™ BCA protein assay kit (Thermo). The supernatant was then mixed with protein loading buffer (NCM Biotech) and boiled at 100 ℃ for 5 min. The same amounts of proteins (30 μg) from all samples were separated by 10% SDS-PAGE gel (Bio-Rad, USA) and transferred onto a PVDF membrane (Immobilon®-P). After blocking in 5% BSA for 1 h at room temperature and incubated overnight at 4 °C with the indicated primary antibodies. Followed by incubation with secondary antibodies for 2 h at room temperature, and visualized by the NcmECL Ultra (A+B) (NCM Biotech) chemiluminescence reagent, GAPDH was used as an internal control. Antibodies against CDK19 were purchased from Proteintech (13761–1-AP, 1:1000) and GAPDH was purchased from Utibody (UM4002, 1:2000). Protein bands were analyzed using Image J software.
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