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Gel electrophoresis reagents

Manufactured by Bio-Rad
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Gel electrophoresis reagents are a set of chemical solutions and buffers used in the process of gel electrophoresis, a widely-used analytical technique for the separation and analysis of biomolecules such as DNA, RNA, and proteins. These reagents facilitate the migration of charged molecules through a gel matrix under the influence of an electric field, allowing for their separation based on their size and charge characteristics.

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15 protocols using gel electrophoresis reagents

1

Molecular Analysis of Apoptosis Pathways

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The culture media and fetal bovine serum were purchased from Life Technologies (Grand Island, NY, USA). The antibodies against the following proteins were obtained from the indicated vendors: cleaved PARP (Asp214) and γH2AX (9718), (Cell Signaling Technology, Temecula, CA, USA); hnRNP A1 (F-8) and hnRNP A2 (EF-67) (Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA); TRF2 (Millipore, Billerica, MA, USA); β-actin (Sigma-Aldrich, St. Louis, MO, USA); MDC-1 (M2444) (Sigma-Aldrich); caspase-7 (9492), -8 (9746), and PARP (9542) (Cell Signaling Technology). The FITC 488–OO-(CCCTAA)3 PNA probe (F1009) was obtained from Panagene (Daejeon, Korea), and etoposide (E1383) was purchased from Sigma-Aldrich. Superscript III reverse transcriptase, TRIzol reagent, and antibiotics were obtained from Gibco-BRL (San Francisco, CA, USA). The broad-spectrum caspase inhibitor Z-VAD-FMK was purchased from Promega (Fitchburg, WI, USA). Gel electrophoresis reagents were obtained from Bio-Rad (Berkeley, CA, USA).
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2

Immunoblotting Protocol for Protein Detection

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Mouse monoclonal anti-K2, clone 3A3 (1:2000, EMD Millipore, Bedford, MA); goat horseradish peroxidase-conjugated anti-mouse IgG (1:2,000) and goat horseradish peroxidase-conjugated anti-rabbit IgG (1:2,000) were from Calbiochem. Vecta-shield with 4′,6-diamidino-2-phenylindole was from Vector Laboratories. Gel electrophoresis reagents were from BioRad.
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3

Characterization of Macrophage Phenotypes

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The following primary antibodies were from Cell Signaling: anti-phospho-Smad3; anti-Smad3; anti-phospho-ERK MAPK; anti-ERK MAPK, and anti-M-CSF Receptor. The FC blocker used was Mouse SeroBlock FcR, which is a rat monoclonal antibody (clone FCR 4G8, BioRad) that specifically recognizes mouse CD16 and CD32, which are cell surface proteins also known as FcRgIII and FcRgII, respectively. Mouse monoclonal anti-K2, clone 3A3 (1:2000, EMD Millipore); anti-F4/80 (1:50, eBioscience); anti-Gr-1 (1:50, AbD Serotec); anti-CD206 (1:50, BioRad); goat horseradish peroxidase-conjugated anti-mouse IgG (1:2,000) and goat horseradish peroxidase-conjugated anti-rabbit IgG (1:2,000) were from Calbiochem. Vecta-shield with 4′,6-diamidino-2-phenylindole was from Vector Laboratories. Gel electrophoresis reagents were from BioRad. CSF-1 was from Thermo Scientific. LPS and CCL2 were from Sigma.
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4

Analytical Chemistry Reagent Procurement

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LB broth and LB agar were from Amresco (Solon, OH). Urea was from Teknova (Hollister, CA). LC-MS pure reagents (water, ethanol, acetonitrile, and methanol) were purchased from J.T. Baker (Radnor, PA). Gel-electrophoresis reagents were from Bio-Rad (Berkley, CA). Iodoacetamide (IAA) was purchased from MP Biomedicals (Solon. OH). All other reagents are from Sigma-Aldrich (St. Louis, MO) unless specified. The gels used for electrophoresis were from Genscript Biotech Corporation (Piscataway, NJ). Separation occurred on a Mighty Small II from Hoefer Inc. (Holliston, MA) and gels were imaged with a Bio-Rad Gel-Doc EZ Imager. DNA Miniprep spin filters were purchased from Bioneer Corporation (Oakland, CA) and the S-Trap mini devices were from Protifi (Huntington, NY). At the time of publication 200 Miniprep columns from Bioneer have a US price of $115 including DNA reagents and bulk miniprep columns from Epoch Life Science (http://www.epochlifescience.com/) can be obtained for $0.42 each without reagents. Hydrophilic–lipophilic balance (HLB) solid phase extraction (SPE) cartridges (10 mg) from Waters (Milford, MA) were used to desalt peptide samples prior to analysis on a Q-Exactive HF from Thermo Fisher Scientific (San Jose, CA) or an ultrafleXtreme MALDI-TOF from Bruker Scientific LLC (Billerica, MA).
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5

Immunostaining and Western Blot Analysis

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Mouse monoclonal anti-K2, clone 3A3(1:2000), was purchased from EMD Millipore (Billerica, Massachusetts); mouse anti-GFP was from Santa Cruz Biotechnology Inc (Santa Cruz, CA); goat horseradish peroxidase-conjugated anti-mouse IgG (1:5000) and goat horseradish peroxidase-conjugated anti-rabbit IgG (1:5000) were from Calbiochem (Billerica, Massachusetts); and Alexa 568-conjugated phalloidin were from Invitrogen. PE-conjugated anti-CD29 and Vecta-shield with 4′,6-diamidino-2-phenylindole was from Vector Laboratories (Burlingame, CA). Gel electrophoresis reagents were from Bio-Rad (Hercules, CA).
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6

CRISPR-Mediated Kindlin-2 Knockout in E0771 and HML2 Cells

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E0771 BC cells were obtained from American Type Culture Collection (ATCC) and maintained according the manufacturer’s protocols. The HML2 cells were kindly provided by Drs. Pollard and Kitamura [26 (link)]. The HML2 cell line was derived from the E0771 cells by serial propagation of the E0771-derived tumors in recipient mice [26 (link)]. Cells were also routinely authenticated by STR DNA fingerprinting analysis. Kindlin-2-KO cells were generated by lentiviral transduction using CRISPR/Cas9 gene editing as described [23 (link),24 (link),25 (link)]. We used two independent and verified Kindlin-2-specific sgRNAs for each of the human and mouse Kindlin-2 and a scrambled sgRNA (i.e., nonsilencing sgRNA, [23 (link),24 (link),25 (link)]). Loss of Kindlin-2 expression was verified by Western blot. For stimulation of cells with growth factors, cells were serum starved in serum-free DMEM growth medium without antibiotics overnight. The next day, the cells were stimulated with either 100 ng/mL EGF (Millipore) or 5 ng/mL TGF-β for 30 min. EGFR inhibitor ZD1839 and TGF-β receptor inhibitor SB431542 were obtained from SelleckChem and used at a concentration of 10 µM for 2 h. Gel electrophoresis reagents were from Bio-Rad.
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7

Comprehensive Protein Analysis Workflow

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We used the following antibodies: rabbit anti pAKT-S473, pAKT-T308, AKT, pERK1/2, ERK1/2, WAVE3 (Cell Signaling Technology); rabbit anti pSMAD3 and SMAD3 (Abcam); mouse anti-GFP (Clontech) (1:1000); goat horseradish-peroxidase-conjugated anti-mouse IgG and goat horseradish-peroxidase-conjugated anti-rabbit IgG (Calbiochem) (1:2000); mouse monoclonal anti-Actin (Sigma) (1:5000); and Alexa-Fluor-Plus-594-conjugated anti-rabbit IgG and Alexa-Fluor-Plus-488-conjugated anti-mouse IgG (Invitrogen). Vecta-shield with DAPI was from Vector Laboratories. Gel electrophoresis reagents were from Bio-Rad.
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8

TNBC Cell Line Generation and Characterization

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TNBC Cell lines were acquired from the American Type Culture Collection (ATCC; Manassas, VA), and maintained according to the manufacturer’s established protocols. Cell lines were also routinely authenticated by short tandem repeat DNA fingerprinting analysis. WAVE3-deficient (W3-KO) cells were generated using two different and verified sgRNAs targeting the human WAVE3 and the mouse Wave3 genes by lentiviral transduction as described previously [11 (link)]. A scrambled (SCRAM) sgRNA was used as negative control [11 (link)]. Generation of the WAVE3-KO cells overexpressing wildtype (WT) or phosphomutant (Y4) were described previously [17 (link)]. GFP-tagged WAVE3 constructs were generated as described previously [17 (link)]. The GFP-recombinant vector or the empty GFP expression control vector was used for stable transfections using standard protocols. We used the following reagents: Doxorubicin, docetaxel and cisplatin, purchased from Sigma (St. Louis, MO) as powders, were dissolved in DMSO and used as described previously [12 (link)]. For proteasome inhibition, cells were treated with GM6001 (Sigma) at 20 µM for 24 h. Gel electrophoresis reagents were from Bio-Rad (Hercules, CA).
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9

Antibody Characterization for Western Blot and Immunofluorescence

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The following primary antibodies were from Cell Signaling Technology: Rabbit anti α-Tubilin (1:1000), mouse anti-p53 (1:1000) and rabbit anti-p53 (1:1000 for WB and 1:500 for immunofluorescence). Mouse monoclonal anti-Kindlin-2, clone 3A3 (1:2000 for WB and 1:500 for immunofluorescence) was from Millipore; rabbit polyclonal anti SerpinB2 (1:1000) and rabbit polyclonal anti Lamin B1 (1:3000) were from Abcam. Goat horseradish peroxidase-conjugated anti-mouse IgG (1:2000) and goat horseradish peroxidase-conjugated anti-rabbit IgG (1:2000) were from Calbiochem. Mouse monoclonal anti-Actin (1:5000) was from Sigma. Alexa Fluor Plus 594-conjugated anti-Rabbit IgG and Alexa Fluor Plus 488-conjugated anti-mouse IgG were from Invitrogen. Vecta-shield with 4′,6-diamidino-2-phenylindole (DAPI) was from Vector Laboratories. Gel electrophoresis reagents were from Bio-Rad.
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10

Thaumatin Characterization and Modification

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Thaumatin was purchased from TCI America (Portland, OR). Reagent grade 8-Anilino-1-naphthalenesulfonic acid (ANS), 2-bromohexanoic acid, guanidine hydrochloride (GuHCl), phosphorus tribromide, sodium nitrite, and trichloroacetic acid (TCA) were purchased from Sigma-Aldrich (St. Louis, MO). Zinc dust (quality level 200) was purchased from Sigma-Aldrich (St. Louis, MO). 2,4-Dinitrophenylhydrazine (DNPH) was purchased from Spectrum Chemical (New Brunswick, NJ). The gel electrophoresis reagents were purchased from Bio-Rad Laboratories (Hercules, CA). DMPO was purchased from the Cayman Chemical Company (Ann Arbor, MI). All solvents used were at least reagent grade. Deionized water (18.2 MΩ/cm) from the Millipore water purification system was exclusively used for the experiment.
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