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28 protocols using labworks image acquisition and analysis software

1

Molecular Characterization of Clostridioides difficile

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PCR amplification of the tcdA, tcdB, and cdtB genes was performed in 25 μl reaction with GoTaq Green Master Mix (Promega, United States), using the primers described in Table 1. Thermocycler conditions were 15 min at 95°C, followed by 30 cycles of 30 s at 94°C, 90 s at 57°C and 60 s at 72°C, with a final extension of 7 min at 72°C. We also designed primers to amplify the complete tcdC gene (Table 1) using the following conditions, 5 min at 94°C, followed by 30 cycles of 1 min at 94°C, 1 min at 42.5°C and 1 min at 72°C, with a final extension of 4 min at 72°C. Products were analyzed by 2.0% agarose electrophoresis, stained with Eva Green 1X (Jena Bioscience, Germany). Additional genotyping of the strains was done by ribotyping as described previously (Bidet et al., 1999 (link)). DNA from a clinical C. difficile strain ribotype 027 (Kindly donated by Dra. Elvira Garza, Monterrey, Mexico) (Camacho-Ortiz et al., 2015 (link)) was included in each run as a reference. Amplification products were subjected to electrophoresis in a 2.5% agarose gel, ethidium bromide stained and analyzed under ultraviolet light using the LabWorks Image Acquisition and Analysis Software (Version 4.5.00.0 for Windows, UVP).
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2

Western Blot Quantification of Protein Expression

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The proteins were resolved on an SDS denaturing polyacrylamide gel and then transferred onto a nitrocellulose membrane. Antibody to AEG-1 or GAPDH was incubated with the membranes overnight at 4°C. The membranes were washed and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies. Protein expression was assessed by enhanced chemiluminescence and exposure to chemiluminescent film. LabWorks™ Image Acquisition and Analysis Software (UVP, Upland, CA) were used to quantify the band intensities. All the antibodies were purchased from Abcam (Cambridge, MA).
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3

Isolation and Analysis of HMGB1 Protein from Liver

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The total cellular protein in the liver tissues was isolated using cell lysis buffer (Beyotime, China), and the cytoplasmic proteins were isolated using a Nuclear and Cytoplasmic Protein Extraction Kit (Beyotime, China) according to the manufacturer’s instructions. Protein concentrations were determined with a Bicinchoninic Acid (BCA) Protein Assay Kit (Beyotime, China). Thereafter, the proteins were stored at −80 °С for western blot analysis.
Total or cytoplasmic HMGB1 in liver tissues was determined by western blotting as described17 (link). Rabbit anti-HMGB1 monoclonal antibody (ab79823, Abcam, UK; 1:5000) was used as the primary antibody, and HRP-conjugated goat anti-rabbit IgG (MultiSciences, China; 1:5000) as the secondary antibody. β-actin was used as an intrinsic quality control. The chemiluminescence was detected by an automatic exposure machine (Syngene, UK). The density of bands was quantified using Labworks image acquisition and analysis software (UVP, Upland, USA).
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4

Protein Extraction and Western Blot Analysis

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The NPC tissues and normal tissues were washed with PBS, added with cell lysates containing with protease inhibitors, shaken at 4°C for 5 min and centrifuged at 4°C for 10 min at the rate 37100 × g. The proteins were extracted from the supernatant by using Qproteome Mammalian Protein Prer kit (QIAGEN, GmbH, Germany). Proteins (50 μg) were obtained for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and then moved to nitrocellulose membranes. Following blocking with skimmed milk and incubated overnight with the following primary antibody IL-6 (Cat# ab9324, 0.4 μg/ml, Abcam, Cambridge, MA, USA), JAK (Cat# ab205223, 1: 500, Abcam, Cambridge, MA, USA), p-JAK (Cat# ab32101, 1: 1000, Abcam, Cambridge, MA, USA), STAT3 (Cat# 119352, 1:600, Abcam, Cambridge, MA, USA), p-STAT3 (Cat# ab76315, 1:2000, Abcam, Cambridge, MA, USA) and CyclinD1 (Cat# ab134175, 1: 10000, Abcam, Cambridge, MA, USA). After washing with tris-buffered saline solution containing Tween 20 (TBST) 4 times (10 min every time), the membranes were incubated with IRDye™ 700DX-labeled IgG (LI-COR Bioscience, NE, USA) antibody (dilution 1:1000, Upstate, NY, USA) at room temperature for 1 h, washed by TBST 4 times and developed with the substrates. The data were analyzed by LabWorks Image Acquisition and Analysis Software (UVP, Inc., Upland, CA, USA) to obtain the relative protein concentration.
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5

Quantification of NR5A2 Protein Levels

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Western blotting was performed to determine NR5A2 protein expression. The total protein was extracted from the PDAC tissues and normal tissues. Proteins were quantitated by the Bradford method according to the manufacturer’s protocol (Bio-Rad, Hercules, CA, USA). Samples (50 μg protein) were resolved on a 10% SDS-PAGE and transferred onto a nitrocellulose membrane. The membranes were probed with antibodies for NR5A2 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). All of the antibodies were purchased from Abcam company and were used at a dilution of 1:500 for anti-NR5A2 and 1:1000 for anti-GAPDH. The LabWorks image acquisition and analysis software (UVP, Upland, CA, USA) was used to quantify band intensities.
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6

Western Blot Analysis of PTEN

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Cells or grinded human tissues were lysed, and their total protein content was extracted and subjected to electrophoresis and western blot analysis as previously reported (12 (link),13 (link)). Antibodies specific for PTEN (rabbit monoclonal; catalog no., 9188; 1:1,000) and β-actin (mouse monoclonal; catalog no., 3700; 1:2,000), and horseradish peroxidase (HRP)-coupled secondary antibodies against rabbit [anti-rabbit immunoglobulin G (IgG), HRP-linked; catalog no., 7074; 1:2,000] and mouse (anti-mouse IgG, HRP-linked; catalog no., 7076; 1:2,000) were obtained from Cell Signaling Technology, Inc. (Danvers, MA, USA) and used following the standard protocols. Densitometric analysis was performed using LabWorks Image Acquisition and Analysis Software (UVP, Inc., Upland, CA, USA) as previously described (13 (link)).
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7

Western Blot Analysis of NEK2 and GAPDH

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Proteins were resolved on an SDS-denaturing polyacrylamide gel and transferred onto nitrocellulose membrane. Membranes were incubated with antibodies against NEK2 and GAPDH overnight at 4°C before blocking with 5% nonfat milk for 2 hr. Next, membranes were washed and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies at 4°C for 2 hr. Protein expression was assessed via enhanced chemiluminescence and band intensities quantified with LabWorks Image Acquisition and Analysis Software (UVP, Upland, CA, USA). All antibodies were purchased from Abcam (Cambridge, MA, USA).
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8

Western Blot Analysis of Protein Expression

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Cell lysates were prepared using radioimmunoprecipitation assay lysis buffer in the presence of protease inhibitors. Protein concentrations were determined using a BCA Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). Primary antibodies against p53 (DO-1) and β-actin were purchased from Abcam. Rabbit anti-human HPV16 E6 antibody (BS1719-R, 1:400) was purchased from BIOSS. Secondary antibody against goat anti-rabbit immunoglobulin G horseradish peroxidase conjugate was purchased from AJ. Proteins (30 μg) were separated on 10% sodium dodecyl sulfate–polyacrylamide gel and transferred to a nitrocellulose membrane (Bio-Rad, Hercules, CA, USA). Then, the membrane was blocked with 5% non-fat milk for 2 h and incubated with primary antibodies. Proteins were detected using enhanced chemiluminescence reagents (Thermo Fisher Scientific). For immunoreactivity, the membrane was rinsed with TBS, incubated overnight at 4°C with a primary antibody, and then washed and incubated for 1 h with secondary antibody. Immunoreactivity was detected using an enhanced chemiluminescence substrate (Thermo Fisher Scientific). Lab Works image acquisition and analysis software (UVP, LLC) was used to quantify band intensities.
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9

Quantitative Western Blot Analysis

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Cell protein lysates were separated using 10% sodium dodecyl sulfate polyacrylamide gels, electrophoretically transferred to polyvinylidene difluoride membranes (Roche Diagnostics, Mannheim, Germany), and then detected using PTEN antibodies (ab107918), pAKT (sc-7985-R). Protein loading was measured using a mouse anti-GAPDH monoclonal antibody (mAbcam 8245). Lab Works Image Acquisition and Analysis Software (UVP, Upland, CA, USA) were adopted to quantify the band intensities.
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10

Western Blot Analysis of PDCD4 Expression

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The proteins were resolved on an SDS denaturing polyacrylamide gel and then transferred onto a nitrocellulose membrane. Antibody to PDCD4 or GAPDH was incubated with the membranes overnight at 4°C. The membranes were washed and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies. Protein expression was assessed by enhanced chemiluminescence and exposure to chemiluminescent film. LabWorks™ Image Acquisition and Analysis Software (UVP, Upland, CA) were used to quantify the band intensities. All the antibodies were purchased from Abcam (Cambridge, MA).
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