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28 protocols using sc 24948

1

Quantification of ANP32A Protein Expression

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To analyse ANP32A expression in gene-edited clonal lines (Supplementary Fig. 3 and Supplementary Fig. 17k), at least 150,000 cells were lysed in 50 µl of 1X RIPA lysis buffer (sc-24948, Santa Cruz Biotechnology) containing protease and phosphatase inhibitor (Halt, Thermo Scientific 78440) according to the manufacturer’s instruction. To analyse ANP32A expression in AKO embryos (Supplementary Fig. 14g), approximately 2 mg of embryonic tissue was lysed in 100 µl of 1X RIPA lysis buffer (sc-24948, Santa Cruz Biotechnology) containing protease and phosphatase inhibitor (Halt, Thermo Scientific 78440) according to the manufacturers’ instruction. Denaturing electrophoresis and western blotting were performed using the NuPAGE electrophoresis system (Invitrogen) following the manufacturer’s protocol. Immunoblotting was performed using the following primary antibodies; rabbit anti-ANP32A (Sigma-Aldrich AV40203; 1/1000 dilution) and mouse anti-ɣ-tubulin (Sigma-Aldrich TS6557; 1/1000 dilution). The following secondary antibodies were used: goat anti-mouse IRDye 800CW (LI-COR 925-32211; 1/10,000 dilution) and goat anti-rabbit IRDye 680RD (LI-COR 925-68070; 1/10,000 dilution). Protein bands were visualised through fluorescence using the Odyssey Imaging System (LI-COR) according to the manufacturer’s instruction.
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2

Evaluating GSNO Catabolism in GSNOR KO Lungs

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GSNOR KO lung tissue was evaluated to confirm diminished GSNO catabolism compared to WT. Lungs from six week old mice were homogenized in ice-cold RIPA lysis buffer containing protease inhibitors (sc-24948, Santa Cruz Biotechnology, Dallas, TX) and protein levels were quantified by Pierce BCA protein assay kit (Thermo Scientific, Rockford, IL). Enzyme activity in lung homogenates was assessed by timed GSNO catabolism and evaluation by GSNO-dependent NADH consumption quantified by absorbance.27 (link)GSNO-dependent NADH consumption: A known quantity of GSNO (100 μM) was loaded with co-reagents (200 μM NADH and 2 mM GSH) and equivalent protein quantities of frozen lung homogenates (100 μg) in PBS. At time 0, 10, 20, 30, and 40 minutes after incubation at 37°C, NADH absorbance (absorption at 340 nm) was measured (FLUOstar Omega spectrometer, BMG Labtech, Ortenberg, Germany) and NADH decrease was calculated and reported as % from time 0.27 (link)
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3

Multifaceted Protein Analysis in Cells

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Cells were lysed in RIPA buffer containing PMSF and protease and phosphatase inhibitors (sc-24948, Santa Cruz Biotechnology) for 30 minutes on ice. Proteins were separated on denaturing 4%–15% SDS-PAGE (4561086, Bio-Rad), transferred onto nitrocellulose membrane (1704270, Bio-Rad) and probed with antibodies to SLC7A5 (5347S), c-MYC (E5Q6W, 18583S), β-actin (13E5, 4970S), S6K1 (49D7, 2708S), pS6K1 Kinase (Thr389) (108D2, 9234S), EEA1 (C45B10, 3288S), RAB7 (D95F2, 9367S), Cathepsin D (2284S), Na/K ATPase (3010S), Tubulin (11H10, 2125S), mTOR (7C10, 2983S), Raptor (24C12, 2280S), RHEB (E1G1R, 13879S), PD-1 (D4W2J, 86163S, all Cell Signaling Technology), CD63 (ab68418), Cathepsin H (ab185935) and VPS39 (ab224671, all Abcam). Membranes were developed using HRP-conjugated secondary antibodies (Cell Signaling Technology) and Chemiluminescent Western Blot Detection Substrate (Thermo Fisher Scientific).
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Protein Extraction and Western Blot Analysis

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The culture medium was removed and the cells were washed with PBS (Mg2+ and Ca2+ free). RIPA buffer was added (cat. no. sc-24948; Santa Cruz, Inc.) and the cells were incubated at 4˚C for 60 min, then centrifuged at 12,000 x g for 20 min 4˚C. The supernatant was the total cell lysate. Proteins were extracted from the HCM-MEC010 and human tongue squamous cell carcinoma (SAS; purchased from the Japanese Collection of Research Bioresources Cell Bank) cell lines as previously described (25 (link)). Protein concentration was measured using a Bradford assay (26 (link)) Western blot analysis was performed as previously described (25 (link)). The primary and secondary antibodies are listed in Table I. The protein expression ratio, compared with that in SAS cells, was measured using ImageJ v1.53e software (National Institutes of Health). The data are presented as the mean ± SD. The experiment was repeated three times.
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5

Western Blot Analysis of ICH in Rats

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Western blotting was performed as previously described [5 (link)]. In brief, rats were anesthetized with isoflurane at the established time points after ICH and transcardially perfused with cold PBS. The right brain hemisphere was homogenized in RIPA lysis buffer (sc-24948, Santa Cruz Biotechnology, USA) and further centrifuged at 14000 rpm for 30 min. Equal amounts of protein (4 μL, 30 μg) were loaded onto a 10% SDS-PAGE gel. After separation, the proteins were transferred to a nitrocellulose membrane, which was further blocked for 2 h with a blocking solution. The membranes were incubated with the following primary antibodies overnight at 4°C: anti-albumin (1 : 500, ab207327, Abcam, USA), anti-p-ERK (1 : 1000, Santa Cruz Biotechnology, USA), anti-ERK (1 : 1000, sc-514302, Santa Cruz Biotechnology, USA), anti-Nrf2 (1 : 1000, GTX103322, Gene Tex), anti–HO-1 (1 : 1000, ab68477, Abcam, MA, USA), anti-Romo1 (1 : 1000, Aviva Systems Biology, San Diego, CA), anti-Bcl2 (1 : 1000, ab59348, Abcam, MA, USA), and anti-Bax (1 : 1000, Littleton, CO). The membranes were incubated with an anti-β-actin antibody (1 : 5000, sc-47778, Santa Cruz Biotechnology, TX, USA).) The results were normalized using β-actin as a loading control. The relative density of the blot bands was quantified by densitometry using the ImageJ software.
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6

Golga5 Mutant Protein Expression Analysis

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Four pairs of E11.5 Golga5E3-4del/E3-4del homozygous and wildtype control embryos and four pairs of Golga5E4-13bp/E4-13bp mutant and control lung and liver tissues from E13.5 embryos were lysed in RIPA buffer containing proteinase inhibitors (Santa Cruz, SC-24948). The supernatant was mixed with Laemmli buffer and separated by SDS-PAGE on 10 % Polyacrylamide gel. Western blots were incubated with rabbit anti-GOLGA5 (Sigma-Aldrich HPA000992; 1:1000) or the anti-β-Actin (Cell Signaling #3700, 1:3,000) antibody followed by washing and incubation with HRP-conjugated secondary antibodies. The signals were detected using Immobilon Western HRP peroxidase solution and Luminol reagents and exposed to X-ray film (Lan et al. 2016 (link)).
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7

Western Blot Analysis of Liver Proteins

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Liver tissues were lysed with radio immunoprecipitation assay buffer (sc-24948; Santa Cruz Biotechnology Inc., Dallas, TX, USA) containing 1% protease inhibitor cocktail (P8340; Sigma-Aldrich, St. Louis, MO, USA) and 2% phenylmethanesulfonyl fluoride (P7626, Sigma-Aldrich). After determining the protein concentration, 40 μg of protein was separated by 10-12% sodium dodecyl sulfate polyacrylamide gel electrophoresis and then transferred onto polyvinylidene fluoride membranes (0.45 μm; GE Healthcare Life Sciences, Marlborough, MA, USA). After blocking with 5% bovine serum albumin at 4°C for 4 h, the membranes were incubated with primary antibodies at 4°C for 12 h and subsequently incubated with the appropriate secondary antibodies at 4°C for 4 h (Table S1). The bands were then visualized using an enhanced chemiluminescence kit (PE0010; Solarbio Science & Technology Co., Ltd, Beijing, China) and a Tanon 5200 gel imaging system (Tanon Science & Technology Co., Ltd., Shanghai, China). ImageJ software (National Institutes of Health, Bethesda, MD, USA) was used to quantify the bands.
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8

Western Blot Analysis of Renal Proteins

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Proteins from renal tissue were homogenized in ice-cold radioimmunoprecipitation assay lysis buffer (pH 7.0; sc-24948; Santa Cruz Biotechnology, Santa Cruz, CA, USA) supplemented with freshly prepared Halt Protease and Phosphatase Inhibitor Cocktail (78446; Thermo Scientific, Waltham, MA, USA). Tissue homogenate was centrifuged at 15,000× g for 15 min at 4 °C. The supernatant was separated for protein quantification, and a total of 30 μg protein was used for detection. Proteins were resolved via SDS-PAGE under reducing conditions unless otherwise noted. After gel electrophoresis, the proteins were electrotransferred from the gel onto polyvinylidene difluoride (PVDF) membranes (0.45-μm PVDF Transfer Membrane; Thermo Scientific). Then, the membrane was blocked with Rapid Block TM solution (VWR Life Science, Radnor, PA, USA) and probed with the indicated antibody. Images were obtained using the Syngene Western Blot Imager G: BOX (Syngene, Cambridge, UK) and analyzed by ImageJ software (NIH, Bethesda, MD, USA).
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9

Western Blot Analysis of Cellular Proteins

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Cells were washed with cold PBS and lysed in commercial RIPA buffer supplemented with phenylmethylsulfonyl fluoride and protease and phosphatase inhibitors (sc-24948, Santa Cruz Biotechnology) for 30 min on ice. Proteins were separated on denaturing 4-15% (15-well) SDS–polyacrylamide gel electrophoresis (4561086, Bio-Rad), transferred onto nitrocellulose or PVDF membrane (1704270, Bio-Rad), and probed with antibodies to TCF1 (C46C7, #2206, 1:1000), β-actin (D6A8, #8457), 1:1000, CISH (D4D9, #8731, 1:1000), LC3B (D11, #3868, 1:1000), COXIV (3E11, #4850, 1:1000, all Cell Signaling Technology), and ATP6V1A (ab199326, Abcam, 1:1000). Blotting membranes were developed by incubation with horseradish peroxidase (HRP)–conjugated secondary antibodies (Cell Signaling Technology, #7074, 1:2500) followed by treating with the Chemiluminescent Western blot Detection Substrate (Thermo Fisher Scientific).
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10

Kidney Protein Lysate Preparation and Western Blot

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Kidney protein lysates were produced by homogenization in lysis buffer containing 50 mM Tris-HCl pH7.4, 0.5%NP40, 150 mM NaCl, 20 mM MgCl2, protease and phosphatase inhibitors (Sigma Aldrich; 4906837001/5892970001), or in supplemented RIPA buffer (Santa Cruz; sc-24948). 1–25 μg protein lysate was reduced by addition of SDS-containing reducing buffer containing 0.1 M DTT and denatured by boiling at 95 °C for 5 min and loaded onto 4–12% Tris-HCl gels (ThermoFisher; NP0323BOX). Proteins were transferred to a nitrocellulose membrane, blocked with 5% BSA or 5% non-fat milk and probed with indicated antibodies. Antibodies; anti-NDRG1 D6C2 mAb (Cell Signaling Technologies; #9408, 1:1000) and anti-rabbit IgG, HRP-linked antibody (Cell Signaling Technology; #7074). Monoclonal anti-β-actin-peroxidase (Sigma; A3854, 1:10000) was used to detect the loading control and ECL prime (Amersham; RPN2232) was used for signal detection.
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