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14 protocols using l7543

1

Western Blot Analysis of Autophagy-Related Proteins

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Western blot assays were performed according to previously described methods.11 The membranes were probed with the following primary antibodies overnight at 4°C: anti‐cathepsin D (CTSD) (1:2000, Abcam, ab75852), anti‐lysosomal‐associated membrane protein 1 (LAMP1) (1:2000, Abcam, ab24170), anti‐phosphorylated protein kinase A (p‐PKA) (1:5000, Abcam, ab32390), anti‐PKA (1:2000, Abcam, ab75993), anti‐phosphorylated extracellular signal‐regulated kinase 2 (p‐ERK2) (1:1000, Abcam, ab201015), anti‐ERK2 (1:1000, Abcam, ab32081), anti‐TFEB (1:1000, Santa Cruz Biotechnology, sc‐48784), anti‐histone 2B (1:2000, Abcam, ab40886), anti‐LC3B (1:1000; Sigma, L7543), anti‐SQSTM1 (1:1000; Abcam, ab91526), anti‐Beclin1 (1:1000, Santa Cruz Biotechnology, sc‐11427), anti‐Atg5 (1:1000; Abcam, ab78073), anti‐phosphorylated TFEB (Ser142) (1:1000; Merck, ABE1971‐l), anti‐peroxisome proliferator‐activated receptor gamma co‐activator 1‐alpha (PGC‐1α) (1:1000; Abcam, ab54481) and anti‐β‐actin (1:5000, Abcam, ab8226). After incubation with horseradish peroxidase‐conjugated secondary antibodies, the membranes were visualized using SuperSignal Chemiluminescent Substrates (Thermo Fisher Scientific, 34080, Massachusetts, USA).
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2

Western Blot Analysis of Autophagy Markers

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Cells were harvested and washed with cold phosphate-buffered saline (PBS). The proteins were extracted with RIPA Cell Lysis Buffer (Beyotime Institute of Biotechnology, Haimen, China) and maintained on ice for at least 30 min. The lysates were centrifuged at 12,000 g at 4 °C for 10 min, and the supernatant was transferred to a fresh tube. After the protein concentration was measured using the bicinchoninic acid (BCA) method, an equal quantity of total protein per lane was separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membranes. The membranes were blocked with 10% non-fat dry milk powder in PBS for 1 h at room temperature and then incubated overnight at 4 °C with specific antibodies against LC3 (1:1000, Sigma, L7543), SQSTM1/p62 (1:1000, Abcam, ab56416), TFEB (1:2000, Bethyl Laboratories, A303–673A), LAMP-1(1:1000, Abcam, ab24170), and ACTB (1:5000, Sigma, A5441). After the membranes were incubated with the primary antibody, they were washed three times in TBST and then incubated with corresponding HRP-conjugated anti-mouse or anti-rabbit (Beyotime, A0208 or A0216) secondary antibody for 1 h at room temperature. Next, the membranes were washed and visualized using a Luminata Forte Western HRP Substrate (Merck Millipore, WBLUF0500). The bands were quantified with Image J software.
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3

Western Blot Analysis of Neuro-2a Cells

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Neuro-2a cells were lysed in ice-cold RIPA Lysis Buffer. The protein concentration of each sample was determined by the bicinchoninic acid (BCA) protein assay (Pierce Biotechnology, Rockford, IL, USA). The samples were denatured by adding 5 × SDS-PAGE Sample Loading Buffer (Beyotime institute of biotechnology, China) and heating for 10 min at 100 °C. Equal amounts of protein were separated by10%–15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred electrophoretically to polyvinylidene fluoride(PVDF) membranes (Millipore, Billerica, MA, USA). After blocking with 5% non-fat milk in Tris-buffered saline (50 mM TRIS-HCl, pH 7.5, 150 mM NaCl) containing 0.2% Tween 20, the membranes were probed with antibodies against the following proteins: LC3B (Sigma, L7543), SQSTM1/P62 (Abcam, ab56416), cleaved caspase-3 (CST, 9661), HIF-1α (Novus, NB100-105), PINK1 (Novus, BC100-494), BNIP3 (Abcam, ab109362), and β-actin (Proteintech, 60008-1-Ig). Following incubation with secondary anti-mouse (Proteintech, SA00001-1) or anti-rabbit (Proteintech, SA00001-2)antibodies, protein bands were visualized using enhanced chemiluminescence(ECL) blotting detection reagents (Millipore, WBKLS0500).
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4

Immunofluorescence Analysis of Autophagy Markers

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Cells were grown on coverslips in 12-well plates (1 × 200 cells/well) overnight and then treated with corresponding chemicals that was performed as previously described. After that, cells were postfixed with 4% PFA for 20 min, then washed with PBS for three times (10 min/time), and then treated with 10% goat or donkey serum diluted in PBS-0.3% Triton X-100 for 30 min at room temperature. Next, cells were incubated with antibodies with P62 (1:500, Sigma, P0067), LC3 (1:200, Santa, sc-376404), LAMP2 (1:200, Abcam, ab25631), LC3 (1:500, Sigma, L7543), SOD1 (1:400, Abcam, ab16831), or Rab7 (1:500, Abcam, ab137029) overnight at 4 °C. The cells were washed with PBS for three times and stained with secondary antibodies, Alexa Fluor 594-conjugated goat anti-rabbit (1:1000, Thermo Fisher, #A-11037) or Alexa Fluor 647-conjugated goat anti-mouse (1:1000, Thermo Fisher; #A-21236), for 1 h at room temperature, then stained nuclei with DAPI Fluoromount-G (Southern Biotech). Finally, imaged the cells by confocal microscopy.
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5

Analyzing Autophagy and Antioxidant Proteins

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The HepG2 cell and the liver tissue lysates were centrifuged for 15 min at 12,000 g, and the resulting supernatant fraction was transferred to a new tube. The protein concentrations were determined using a Bradford protein assay kit (Beyotime Company, P0006). The protein samples were separated by SDS-PAGE. Following protein transfer to PVDF membranes, the membranes were blocked and then incubated overnight at 4°C with antibodies against LC3(1:1000; Sigma, L7543), SQSTM1/p62 (1:1000; Abcam, ab56416), SIRT3 (1:100; Santa Cruz Biotechnology, sc-99143), SOD2 (1:100; Santa Cruz Biotechnology, sc-33254), and ACTB (1:5000; Sigma, A5441) The membrane was visualized by enhanced chemiluminescence using Super Signal West Pico blotting (Pierce, 34079) detection reagents and exposure to Hyper Performance Chemiluminescence film.
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6

Western Blot Analysis of Autophagy and Lipid Metabolism

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Cells were lysed in IP buffer containing phenylmethylsulfonylfluoride (PMSF), and proteinase inhibitors for 30 min on ice. The cell lysates were centrifuged at 10,000 rpm for 10 min at 4 °C to collect supernatants. Protein concentrations were measured with BCA protein assay kit. Proteins were electrophoresed and transferred to PVDF membranes and incubated with antibody. Finally, the bands were quantified using ImageJ software. The following primary antibodies: P62 (1:1000, Sigma, P0067), LC3 (1:1000, Sigma, L7543), SOD1 (1:2000, Abcam, ab16831), HMGCR (1:200, Santa, sc-271595), FDPS (1:100, Proteintech, 16129-1), RABGGTA (1:100, Proteintech, 14448-1), Rab7 (1:500, Abcam, ab137029), and β-actin (1:1000, Proteintech, 60008-1).
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7

Western Blot Analysis of Autophagy Markers

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The appropriate amounts of proteins were applied and subjected to SDS‐PAGE. The membranes were incubated with primary antibodies at 4°C overnight after proteins were transferred to 0.22 µm PVDF membranes (ISEQ00010, Millipore) and blocked with 5% nonfat dry milk in TBST. The bands were detected with an EZ‐ECL kit (BI biological industries, 20‐500‐120) in Imagequant LAS400 mini (GE Healthcare) equipment after incubation with secondary antibodies.
Primary antibodies to Beclin1 (cell signaling technology, 3738), LC3 (Sigma‐Aldrich, L7543), p53 (Abcam, ab1101), pRB (Abcam, ab32015), Atg5 (Cell Signaling Technology, 8540), Atg16L1 (Sigma‐Aldrich, A7356), LAMP1 (Abcam, ab24170), SPATA18 (Abcam, ab107702), Atg9B (Thermofisher Scientific, PA5‐20998), RGS19 (Abcam, ab72085), HA (Sigma‐Aldrich, H9656), Flag (Sigma‐Aldrich, F7425), GAPDH (Abcam, ab9485), ACTB (Abcam, ab8224), Histone H3 (Abcam, ab1791), and Na‐K ATPase (Abcam, ab76020) were applied in our study. HPR‐labeled secondary anti‐mouse (115‐035‐003) and anti‐rabbit (111‐035‐003) antibodies were purchased from Jackson Immunoresearch Laboratories.
Subcellular extraction was collected with subcellular protein fraction kit for cultured cell (Thermofisher Scientific, 78840).
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8

Molecular Assessment of Traumatic Brain Injury

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Mice were anesthetized with 1.5% pentobarbital sodium at a dose of 50 mg/kg, perfused with ice-cold saline and then decapitated. Approximately 5 mm of the injured cortex was collected and homogenized in RIPA buffer (Thermo Fisher Scientific, 89901, Waltham, MA, USA) containing protease (Roche, 11836170001) and phosphatase (Sigma, P5726, St. Louis, MO, USA) inhibitors. Homogenates were centrifuged at 20,000 g for 20 min at 4 °C to collect the lysates. Protein concentrations were measured using BCA reagent (Thermo Fisher Scientific, 23225). Proteins (20 μg per sample) were resolved on 12% SDS-PAGE gels and then transferred to PVDF membranes (Millipore, IPVH00010, Massachusetts, USA). The Membranes were blocked with 5% nonfat milk and probed with the following primary antibodies overnight at 4 °C: anti-LC3B (1:1000; Sigma, L7543), anti-SQSTM1 (1:1000; Abcam, ab91526), anti-SQSTM1 (1:1000; Abcam, ab56416), anti-Beclin1 (1:1000, Santa Cruz Biotechnology, sc-11427), anti-Atg5 (1:1000; Abcam, ab78073), and anti-β-actin (1:1000; Abcam, ab8226). After an incubation with HRP-conjugated secondary antibodies, membranes were visualized using SuperSignal Chemiluminescent Substrates (Thermo Fisher Scientific, 34080).
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9

Immunofluorescence Imaging of Tumor Cells

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For immunofluorescence, tumor cells were obtained as described in Rowald et al. (2016) (link). Cells were cultured on coverslips coated with Collagen I (Cultrex, 344.020-01). After 24 h, cells were fixed with 4% PFA for 10 min at room temperature or with a methanol/acetone mix for 10 min at −20°C and permeabilized with 0.2% Triton X-100 PBS for 10 min. Cells were treated with blocking buffer containing 5% donkey serum, 1% BSA, and 0.2% Triton X-100 in PBS for 1 h at RT. The following primary antibodies were used: rabbit anti-LC3 (1:100, Sigma, L7543), rabbit anti-Fibronectin (1:40, Abcam, ab23750), mouse anti-Ataxin1 (1:50, Santa Cruz, sc-365343), mouse anti-Myosin X (1:50, Santa Cruz, sc-166720), mouse anti-RhoA/RhoC (1:100, Thermo Scientific, 1B3-4A10), mouse anti-Vimentin (1:50, Sigma, V2258), and rabbit anti-AKT3 (1:800, Cell Signaling, E1Z3W). Donkey anti-mouse Alexa 488 and anti-rabbit Alexa 568 secondary antibodies were used (1:500, Invitrogen), and the DNA was stained with DAPI. Images were acquired with the Leica LAS 4.5 software on a Leica SP5 confocal microscope. Quantification of LC3 fluorescence intensity was performed with ImageJ software.
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10

Protein Expression Analysis Protocol

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Proteins were extracted using a bicinchoninic acid (BCA) protein assay kit (Thermo Fisher Scientific, 23225, Waltham, MA, USA). Equal amount of proteins (40 μg) were separated by 10 or 12% SDS-PAGE and then transferred to PVDF membranes. After blocking by 5% nonfat milk, the membranes were incubated with primary antibodies overnight at 4 °C, and then washed three times (10 min/time), subsequently with secondary antibodies for 1 h at room temperature. Finally, the bands on the membranes were scanned with an Odyssey Infrared Imaging System (LI-COR, Lincoln, NE, USA), and quantities analysis was performed with ImageJ.
The primary antibodies: P62 (1:1000, Sigma, P0067), LC3 (1:1000, Sigma, L7543), SOD1 (1:2000, Abcam, ab16831), HMGCR (1:200, Santa, sc-271595), FDPS (1:100, Proteintech, 16129-1), RABGGTA (1:100, Proteintech, 14448-1), Rab7 (1:500, Abcam, ab137029), and β-actin (1:1000, Proteintech, 60008-1).
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