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76 protocols using ab128915

1

Quantitative Analysis of Integrin β1 and PAG1

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Total RNA was extracted from cells and tissues using Trizol reagent (Invitrogen).qPCR was performed with the SYBR-Green Real-Time PCR Master Mix kit (Toyobo, Osaka, Japan). Primers were as follows: GAPDH (for internal control), 5′-CCAACCGCGAGAAGATGA-3′ (upper) and 5′-CCAGAGGCGTACAGGGATAG-3′ (lower); integrin β1, 5′-GACGCCGCGCGGAAAAGATG-3′(upper) and 5′-GCACCACCCACAATTTGGCCC-3′ (lower); and PAG1, 5′-GAGTCCACCTACACCTCCATTC-3′ (upper) and 5′-GCCTTTTCTTCCTCTCTGTTGA-3′ (lower). Total protein was extracted and subjected to 10% SDS-PAGE and Western blotting, as previously described 16 (link). The following antibodies were used: anti-integrin β1 (ab24693; 1:1000), anti-PAG1 (ab155100; 1:1000), and anti-GAPDH (ab128915; 1:2000) (All from Abcam; Cambridge, MA, USA).
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2

Protein Quantification and Analysis in EV Samples

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Total protein content was extracted from SH-SY5Y cells or EVs using RIPA kits (R0010, Solarbio, Beijing, China). Briefly, 40 µg of each sample was extracted, separated with 10% SDS-PAGE, and electrotransferred onto a PVDF membrane (Merck Millipore, Billerica, MA, USA). Subsequently, the membrane was blocked and incubated with the following primary antibodies: EGR1 (dilution ratio of 1:1000, #4154, CST, Beverly, MA, USA), NOX4 (dilution ratio of 1:2000, ab109225, Abcam), p–p38 (dilution ratio of 1:1000, #4511, CST), P38 (dilution ratio of 1:1000, #8690, CST), TH (dilution ratio of 1:5000, ab137869, Abcam), 4-HNE (dilution ratio of 1:1000, ab46545, Abcam), and GAPDH (dilution ratio of 1:10000, ab128915, Abcam). Afterward, the membrane was incubated with IgG (dilution ratio of 1:10000, ab97051, Abcam). Later, the membrane was developed using an electrogenerated ECL, and then the membrane was exposed to light using the Image Quant LAS 4000 C gel imager (GE Company, Schenectady, NY, USA) and analyzed with the ImageJ software (1.48 u, National Institutes of Health, Maryland).
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3

Quantifying NEAT1 and SFPQ Expression

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RT-qPCR of NEAT1_2 and SFPQ mRNA in tissue specimens or cell lines were performed using a custom-made RT-qPCR kit (GeneCopoeia, Maryland, USA), following the manufacturer’s instructions. The semi-quantitative 2−ΔΔCt method was employed for qPCR data analysis, and expression levels of NEAT1_1, NEAT1_2 or SFPQ mRNA in each sample were normalized to that of GAPDH mRNA before further analysis. Western blotting of SFPQ in different cell cultures was performed using a rabbit anti-human SFPQ monoclonal antibody (ab177149), rabbit anti-human GAPDH monoclonal antibody (ab128915) and horseradish peroxidase-conjugated goat anti-rabbit second antibody (ab205718, Abcam, Cambridge, UK), following the manufacturer’s instructions. Western blotting results were further analyzed by normalizing the gray scale of the SFPQ band in each sample to that of GAPDH using ImageJ software before statistical analysis.
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4

Protein expression analysis of HER2, GAPDH, and p21

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Primary antibodies recognizing HER2 (c-ERBB-2) (CB11, #MU134-UCE, BioGenex), human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (#Ab128915, Abcam), and p21 (#Ab11CP74, NeoMarkers) were used. As secondary antibodies, we used enhanced chemilumi-nescence (ECL) rabbit IgG, horseradish peroxidase (HRP)–linked whole antibody (from donkey, #NA934–1ML, Amersham GE Healthcare) and ECL mouse IgG, HRP-linked whole antibody (from sheep, #NA931, Amersham GE Healthcare).
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5

Western Blot Analysis of Protein Markers

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After the protein extraction and quantification using the radio immunoprecipitation assay (RIPA) buffer and BCA protein determination kit (Sigma), 40 µg proteins were separated by using sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE). Subsequently, we transferred the proteins onto the polyvinylidene fluoride membranes (Millipore) and Western Blocker™ solution (Sigma) was employed for preventing the non-specific combination, followed by the incubation of primary antibodies (overnight at 4 °C) and secondary antibody (at the room temperature for 1 h). Ultimately, the immune binding was discerned using the ECL Western HRP Substrate (Millipore), and analyzed with ImageLab software version 4.1 (Bio-Rad, Hercules, CA, USA). The antibodies were from Abcam (Cambridge, UK): anti-ki67 (ab16667, 1:1000), anti-E-cadherin (ab40772, 1:1000), anti-Fibronectin (ab32419, 1:1000), anti-matrix metalloproteinase 9 (anti-MMP9; ab219372, 1:1000), anti-PD-L1 (ab228415, 1:1000), internal control anti-GAPDH (ab128915, 1:3000) and anti-rabbit IgG/HRP-linked secondary antibody (ab205718, 1:5000).
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6

NLRP1 Activation and Autophagy Signaling

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The NLRP1 activator muramyl dipeptide (MDP) (Selleck, USA) was then added at 100 μmol for 24 hours to the oxidative stress model according to the preliminary experiment and the published studies [21 (link)–24 (link)]. The cell viability determination was the same as that in Section 2.1.
Total protein from HTR-8/SVneo cells was prepared with RIPA lysing buffer. The sample proteins (20 μg) of the different groups were separated using 10% SDS-PAGE and transferred onto PVDF membranes. These membranes were incubated with a primary antibody, followed by incubation of the anti-rabbit IgG secondary antibody. Protein expression was detected with an enhanced chemiluminescence detection kit. GAPDH served as an internal control. The antibodies included those for IL-1β (Abcam, ab216995), pro-IL-1β (Abcam, ab216995), pro-CASP1 (Abcam, ab207802), CASP1 (Abcam, ab207802), Beclin-1 (Abcam, ab207612), LC3 (Abcam, ab51520), p62 (Abcam, ab211324), ATG5 (Abcam, ab108327), ATG7 (Abcam, ab52472), NLRP3 (Abcam, ab263899), NLRP1 (BioLegend, 679802), and GAPDH (Abcam, ab128915). An ECL chemiluminescent reagent and imaging system (Bio-Rad, USA) were used to display protein bands, with the collected images analyzed using Bio-Rad software.
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7

Protein Quantification and Western Blot Analysis

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A549 or SPC‐A1 cells after transfection were lysed in order to extract protein. The concentrations of protein samples were evaluated with the bicinchoninic acid assay kit (Pierce). All extracted proteins were isolated by 10% SDS‐PAGE (Bio‐Rad Laboratories) and later transferred to polyvinylidene fluoride membranes (Millipore). After being treated with primary antibody against MYBL2 (0.8 μg/mL, AV100748, Sigma‐Aldrich) or GAPDH (1/20 000, ab128915, Abcam) and secondary antibodies, immunoreactive bands were exposed via ECL method.
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8

Protein Detection and Quantification Assay

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The Western analysis assays for p53, Vinculin, and GAPDH detection were performed as previously described (18 (link)). Briefly, mixtures of 1 mg ml−1 cell lysates and the fluorescent master mix were heated at 95 °C for 5 min. The samples and all other reagents were dispensed into the microplates and capillary electrophoresis Western analysis was carried out with the ProteinSimple WES instrument and analyzed using the inbuilt Compass software (ProteinSimple). DO-1 mouse anti-p53 antibody (1:400, Santa Cruz sc-126), mouse anti-vinculin antibody (1:600, R&D Systems MAB6896), and rabbit anti-GAPDH (1:800, Abcam ab128915) were used.
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9

Western Blot Analysis of Cellular Proteins

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The cells were lysed using RIPA buffer (150 mM NaCl, 50 mM Tris-HCl at pH 7.4, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate and 1% NP-40) mixed with a protease and phosphatase inhibitor cocktail (Roche Diagnostics GmbH, Mannheim, Germany) and phenylmethylsulfonyl fluoride (PMSF) (Biosharp, Hefei, China) for 15 min on ice. The proteins were subjected to western blotting according to standard protocols. Antibodies were as follows: SIRT2 (HPA011165,Sigma), SIRT2 (s8447, Sigma), cMYC (ab32072, Abcam, Cambridge, UK), p293-PDHA1 (ab92696, Abcam), GAPDH (ab128915, Abcam), cleaved-caspase3 (9664s, CST, Danvers, MA, USA), cleaved-PARP (5625s, CST), PDHA1 (ab110334, Abcam), PHGDH (14719-1-AP, Proteintech, Chicago, IL, USA), PSAT1 (10501-1-AP, Proteintech), PSPH (14513-1-AP, Proteintech), HRP-conjugated anti-rabbit (7074, CST), and anti-mouse antibodies (7076, CST).
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10

Western Blot Analysis of FOXA1 Protein

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Total cellular protein was isolated with RIPA buffer containing protease and phosphatase inhibitors. After centrifugation for 5 min at 4°C, the supernatant was collected and subjected to the quantification of total protein by the Bicinchoninic Acid Assay (Beyotime Institute of Biotechnology, Inc., Shanghai, China). Equal amounts of protein were separated by SDS-PAGE in 10% polyacrylamide gels and transferred to polyvinylidene fluoride membranes (Millipore Inc.). Prior to overnight incubation with primary antibodies, the membranes were blocked with 5% nonfat milk at room temperature for 2 h. The membranes were rinsed with Tris-buffered saline containing 0.1% of Tween 20 (TBST) thrice and next incubated at room temperature for 1 h with a horseradish peroxidase–conjugated secondary antibody (ab205718; 1:5000 dilution in TBST; Abcam, Cambridge, UK, USA). Finally, the protein signals were detected by means of the SuperSignal West Pico Chemiluminescent Substrate Kit (Pierce; Thermo Fisher Scientific, Inc.). Antibodies against FOXA1 (ab170933; Abcam) and GAPDH (ab128915; Abcam) (primary antibodies) were acquired from Abcam and were applied at 1:1000 dilution in TBST. Quantity One software version 4.62 (Bio Rad Laboratories, Inc., Hercules, CA, USA) was applied to analyze the densitometry.
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