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6 protocols using pdquest software v 8

1

Differential Protein Expression Profiling

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The gels were scanned using ChemiDoc™ MP Imaging System (Bio-Rad) at three different settings (Cy2, blue laser 488 nm and 520 bp 40 filter; Cy3, green laser 532 nm and 580 bp 30 filter; Cy5, red laser 633 nm and 670 bp 30 filter). The scanned gels were semi-automatically matched and analyzed by the PD-Quest software v.8.0.1 (Bio-Rad). Spot volumes (pixels*spot size) were assigned to each protein spot and normalized to internal standard. In our experimental design, besides Cy2 labeled internal pooled standard, we also run Cy3 or Cy5 labeled F1 pool in each gel. Therefore, we had two internal controls which enabled better alignment of gels for more accurate spot analysis. For proteome profile comparison, proteome profile of each six Ishak fibrotic stage (F1-F6) was compared to each other by Student’s t-test in search for differentially expressed spots between stages. The quantitative difference in percent volume of spots more than two fold was considered as differential expression change. Competent spots with a p-value ≤0.05 were considered statistically significant and withheld for protein identification by mass spectrometry.
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2

Immunoblot detection of LM-binding proteins

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Immunoblot detection of LM-binding proteins was performed as previously described [14 (link),51 (link)] with minor modifications. In brief, the proteins in the 2D gels were transferred to a nitrocellulose membrane using a constant amperage of 400 mA for 90 min at 4 °C. The blot was blocked for one hour at room temperature with 2% BSA diluted in PBST and incubated overnight at 4 °C with 5 µg/mL of LM (Santa Cruz Biotechnology, Dallas, TX, USA) diluted in blocking solution. LM binding was detected by adding an anti-LM primary antibody raised in rabbit (Abcam, Cambridge, UK) followed by HRP-conjugated anti-rabbit IgG (Sigma, St. Louis, MO, USA). Primary and secondary antibodies were diluted 1:2000 and 1:4000, respectively, in blocking solution and incubated for 90 min at 37 °C. Membranes were washed three times with PBST between antibody incubations and protein spots with bound LM were detected using enhanced chemiluminescence (Clarity Western ECL Substrate, BioRad, Hercules, CA, USA) on a ChemiDoc MP Imaging System (BioRad, Hercules, CA, USA). Spot matching between the silver-stained gel and the counterpart blot was performed using the PDQuest Software v.8.0.1 (BioRad, Hercules, CA, USA).
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3

Proteomic Profiling of PLG Interactome

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The proteins in the 2D gels were transferred to nitrocellulose membranes using a constant amperage of 400 mA for 90 min at 4 °C. Blots were blocked for one hour at room temperature with 2% BSA diluted in PBST and incubated overnight at 4 °C with 25 μg/ml of PLG (Origene) diluted in blocking solution. PLG binding was detected by adding an anti-PLG primary antibody raised in sheep (Acris Antibodies) followed by HRP-conjugated anti-sheep secondary antibody (Sigma). Primary and secondary antibodies were diluted 1:1000 and 1:2000, respectively, in blocking solution and incubated for 90 min at 37 °C. Membranes were washed three times with PBST between incubations and protein spots with bound PLG were revealed with 4-chloro-naphtol following standard procedures. Blots were imaged in a Chemidoc gel-imaging system (BioRad) and spot matching between silver-stained gels and the blots and the assignment of molecular weights and isoelectric points of each protein were performed using the PDQuest Software v.8.0.1 (BioRad).
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4

Western Blot Analysis of tPA and uPA

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Western blot analyses were performed as described in detailed previously [23 (link)] with slightly modifications. CnAOEC and CnAOSMC previously treated with 1μg/ml of rDiACT or rDiFBAL for 24 h were lysed in ice-cold lysis buffer (20mM Tris—HCl (pH 7.5), 140mM NaCl, 10mM ethylendiaminetetraacetic acid, 10% glycerol, 1% Igepal CA-630, aprotinin, pepstatin, and leupeptin at 1μg/ml each, 1mM phenylmethylsulfonyl fluoride, and 1mM sodium orthovanadate). Non-stimulated cells were used as controls under the same conditions. Protein samples (10 μg) were separated by SDS-PAGE under reducing conditions and electrotransferred onto polyvinylidine difluoride membranes. Then, membranes were blocked before incubation with the following primary rabbit polyclonal antibodies: anti-tPA and anti-uPA (Santa Cruz Biotechnology Inc) according to the manufacturer's recommendations. After incubation with HRP-conjugated anti-rabbit secondary antibodies, bands were visualized by a luminol-based detection system with p-iodophenol enhancement. Anti-α-tubulin antibody (Oncogene Research Products) was used as control to confirm loading of comparable amount of protein in each lane. Protein expression was quantified by densitometry using the PDQuest Software v.8.0.1 (Bio-Rad).
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5

Identification of FhES Plasminogen-Binding Proteins

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To determine which proteins of FhES extract bind plasminogen, they were electrotransferred from 2D gels to nitrocellulose membranes at 20 V for 30 min using a Trans-Blot SD Semi-Dry Transfer cell (Bio-Rad). Blots were blocked with 2% BSA in PBS wash buffer, for 1 h at room temperature. FhES membranes were incubated overnight at 4 °C with 10 µg mL−1 of human plasminogen. Then, the blots were incubated with a sheep anti-human plasminogen IgG (Acris Antibodies) at 1:1000 dilution and with a peroxidase-conjugated donkey anti-sheep IgG (Sigma) at 1:2000 dilution. These incubations were performed at 37° C for 90 min with shaking and between each step washed three times with washing buffer for 5 min per wash. Protein bands were revealed with 4-chloro naphthol. Negative controls were also used in which the plasminogen had been omitted. Membranes were digitized with the scanner GS-800 Densitometer (Bio-Rad) using the Quantity One Software v.4.6.5 (Bio-Rad). Matching of 2-D gels with the homologous Western blot to identify plasminogen-binding proteins, the assignment of molecular weights (MW) and isoelectric points (pI) of each protein were analysed using the PDQuest Software v.8.0.1 (Bio-Rad). All assays were performed in triplicate to assess the reproducibility of the spot pattern.
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6

Two-Dimensional Protein Profiling

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Protein samples were obtained in 20 mM Tris-HCl pH 7.6, 0.5 M Sucrose, 0.15 M KCl, 10 μg/ml leupeptin, 2 μg/ml aprotinin, 10 mg/ml PMSF and 20 mM DTT supplemented with the commercial Mini EDTA-free protease inhibitor cocktail (Roche). Proteins were quantified by the Bradford assay and 300 μg of total cellular proteins was used in each isoelectrofocusing (IEF) strip (18 cm ReadyStrip™ IPG Strips pH 3-10 nonlinear). The IEF program and the two dimensional electrophoresis (2-DE) conditions were performed as detailed in [14] (link). Gels from 2-DE were stained with SYPRO Ruby and further digitalized with the FX ProPlus Multiimager. The analysis of the differential intensity spot and the spot volume, normalized by the total density in gels, was quantified by using the PDQuest software (v.8.0.1) (Bio-Rad Laboratories, California, USA). Protein samples from four independent experiments were run in triplicate.
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