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54 protocols using odyssey v3

1

Western Blot Analysis of Apoptosis Markers

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Cells were lysed in the presence of protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN, USA). Whole-cell lysates were subjected to SDS-polyacrylamide gel electrophoresis, electrophoretically transferred onto polyvinylidene difluoride (PVDF) membranes (Thermo Fisher Inc., Rockford, IL, USA) and immunoblotted with anti-Bcl-2 (ab692, Abcam, Cambridge, MA, USA), -Bcl-xL (2764), -Mcl-1 (4572), -PARP (9542), -Bim (2819), -γH2AX (2577), -Bak (3814), -Bax (2774), -cleaved caspase-3 (9661, designated -cf caspase-3, Cell Signaling Technology, Danvers, MA, USA) or -β-actin (A2228, Sigma-Aldrich) antibody, as previously described.22 (link),23 (link) Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li-Cor, Lincoln, NE, USA), as described by the manufacturer. Western blots were repeated at least three times and one representative blot is shown. Densitometry measurements were made using Odyssey V3.0 (Li-Cor), normalized to β-actin, and calculated as the fold-change compared to the corresponding no drug treatment control.
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2

Extracellular Vesicle Protein Isolation and Characterization

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Protein isolation and Western blot were carried out in the same manner as previously described [46 (link),47 (link),48 (link)]. Proteins from EVs were extracted with RIPA buffer (10 mM Tris, 150 nM NaCl, 1% deoxycholic acid, 1% Triton X, 0.1% SDS, and 1 mM EDTA) containing protease inhibitors (aprotinin, PMSF, and sodium orthovanadate). A PierceTM bicinchoninic acid (BCA) protein assay kit was used to assess protein content (Thermo Fisher Scientific, Waltham, MA, USA). A 4–20% Tris-Glycine gel (Bio-Rad, Hercules, CA, USA) was loaded with equal quantities of protein (20 g/lane) and electrophoresed under nonreducing conditions. Proteins were transferred to a PVDF membrane, blocked for 2 h in blocking buffer (PBS, 0.05 percent Tween20®, 5% milk), and then probed overnight with the following primary antibodies: ALIX (Sc-166952; Santa Cruz, CA, USA); CD81 (Sc-7637; Santa Cruz); and GM130 (#12480; Cell Signaling, Danvers, MA, USA). The membranes were rinsed the next day and treated for 1 h at room temperature (RT) with the secondary antibodies donkey anti-mouse IRDye 800CW and donkey anti-rabbit IRDye 680RD (1:2000, LI-COR Biosciences, Lincoln, NE, USA). All antibodies were diluted according to the manufacturer’s instructions. A fluorescence scanner was used to photograph the membranes (Odyssey v.3.0, LI-COR Biosciences).
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3

Western Blot Analysis of Apoptosis Markers

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Cells were lysed in the presence of protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN, USA). Whole-cell lysates were subjected to SDS-polyacrylamide gel electrophoresis, electrophoretically transferred onto polyvinylidene difluoride (PVDF) membranes (Thermo Fisher, Inc., Rockford, IL, USA), and immunoblotted with anti-Mcl-1 (4572), -PARP (9542), -Bim (2819), -Bak (3814), -Bax (2774), -c-Myc (5605s), -cleaved caspase-3 (9661, designated -cf-Cas3; Cell Signaling Technology, Danvers, MA, USA), or -β-actin (A2228; Sigma-Aldrich) antibody, as previously described.37 (link),38 (link) Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li-Cor, Lincoln, NE, USA), as described by the manufacturer. Western blots were repeated at least three times, and one representative blot is shown. Densitometry measurements were made using Odyssey V3.0 (Li-Cor), normalized to β-actin, and calculated as the fold change compared to the corresponding no drug treatment control.
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4

Western Blot Protein Detection Protocol

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Total cell lysates were prepared in RIPA buffer (150 mM NaCl, 50 mM Tris—HCl pH 7.4, 2 mM EDTA, 0.5% deoxycholate, 1mM Na3VO4, 20 mM NaF, 0.5%Triton X-100), supplemented with protease inhibitor cocktail (Roche Applied Science) and phenylmethylsulfonyl fluoride (PMSF). Lysates were cleared by centrifugation at 4°C for 10 min at 10,000 × g. Equal amounts of protein were subjected to electrophoresis on 10% SDS-polyacrylamide gels and then transferred to nitrocellulose membranes (Whatman, Dassel, Germany) using an electroblotting apparatus (Bio-Rad Laboratories, Hercules, CA, USA). Primary antibodies used were the polyclonal anti-Gpnmb (R&D Systems) and anti-tubulin-alpha (Cedarlane Laboratories Limited). Matching secondary IRDye-conjugated antibodies (Westburg) were used for detection in an Odyssey V3.0 (LI-COR Inc.).
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5

Western Blot Analysis of Apoptosis Markers

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Cells were lysed in the presence of protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN, USA). Whole cell lysates were subjected to SDS‐polyacrylamide gel electrophoresis, electrophoretically transferred onto polyvinylidene difluoride membranes (Thermo Fisher Scientific, Waltham, MA, USA) and immunoblotted with anti‐Bcl‐2 (Abcam, Cambridge, MA, USA), ‐Bcl‐xL, ‐Mcl‐1, ‐PARP, ‐Bim, ‐Bak, ‐Bax, ‐cleaved caspase‐3 (designated ‐cf‐Cas3; Cell Signaling Technology, Danvers, MA, USA), or ‐β‐actin (Sigma‐Aldrich) antibody, as previously described.41, 42 Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li‐Cor, Lincoln, NE, USA), as described by the manufacturer. Western blots were repeated at least 2 times and one representative blot is shown. Densitometry measurements were made using Odyssey V3.0 (Li‐Cor), normalized to β‐actin, and calculated as the fold change compared to the corresponding no drug treatment control.
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6

Western Blot Analysis of Apoptosis Markers

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Cells were lysed in the presence of protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN). Whole cell lysates were subjected to SDS-polyacrylamide gel electrophoresis, electrophoretically transferred onto polyvinylidene difluoride (PVDF) membranes (Thermo Fisher Inc., Rockford, IL) and immunoblotted with anti-Bcl-2 (ab692, Abcam, Cambridge, MA), -Bcl-xL (2764), -Mcl-1 (4572), -PARP (9542), -Bim (2819), -γH2AX (2577), -cleaved caspase-3 (9661, designated -cf caspase-3, Cell Signaling Technology, Danvers, MA), or -β-actin (A2228, Sigma-Aldrich) antibody, as previously described (21 (link), 22 (link)). Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li-Cor, Lincoln, NE), as described by the manufacturer. Western blots were repeated at least 3 times and one representative blot is shown. Densitometry measurements were made using Odyssey V3.0 (Li-Cor), normalized to β-actin, and graphed as the fold change compared to the corresponding no drug treatment control.
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7

TIN2 Coimmunoprecipitation Protocol

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Coimmunoprecipitations were conducted similarly to the method previously described (7 (link)). For TIN2 coimmunoprecipitations with TRF1, TRF2, or TPP1, 3 × 106 HEK 293T cells were cotransfected with 5 μg of each plasmid using the Lipofectamine and Plus reagent (Invitrogen) according to the manufacturer's instructions. Twenty-four hours after transfection, the cells were lysed as described above for immunoblotting. Half a percent of the supernatant was reserved as input. Supernatants were incubated overnight at 4°C with 60 μl of mouse monoclonal anti-FLAG M2 magnetic beads (Sigma-Aldrich) or 2 μg of mouse monoclonal anti-Myc 9E10 (Abcam). For myc pulldowns, 60 μl of protein G Plus-agarose beads (Calbiochem) was added during the final hour. Beads were washed four times with a 1:1 dilution of lysis buffer prior to elution with Laemmli loading buffer. Proteins were analyzed by immunoblotting. Western blots were quantified using Odyssey V3.0 (Li-Cor).
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8

Western Blot Analysis of Glycosomal Proteins

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The cells harvested from RNAi studies were directly denatured in 1x Laemmli buffer and analyzed by 12% SDS-PAGE. Proteins were transferred to nitrocellulose membranes (Amersham Biosciences) by standard immunoblotting procedure. The membranes were blocked with 5% (w/v) low-fat milk powder to prevent non-specific binding of antibodies and probed with primary antibodies raised in rabbits against purified Trypanosoma proteins. To assess the effect of RNAi, α-TbAldolase, α-TbPFK, α-TbPEX5, α-TbPEX7, α-TbPEX14 and α-TbPEX11 were used as glycosomal markers, while α-TbEnolase was used as cytosolic marker and loading control (each antibody used at 1:10,000 dilution in PBST i.e., PBS containing 1% BSA and 0.05% Tween20). Following the binding of primary antibodies at 4°C overnight under continuous shaking and washing of the membranes, secondary antibody (goat anti-rabbit IRDye 800CW, LI-COR, dilution 1:15,000 in PBST without BSA) was added to the membrane for 1 h at room temperature with continuous shaking. Immunodetection of proteins was performed using the Odyssey Infrared Imager and the software Odyssey V3.0 (Li-Cor Biosciences GmbH, Bad Homburg).
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9

Immunoblotting for Apoptosis Regulators

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Proteins were subjected to SDS-polyacrylamide gel electrophoresis, and then electrophoretically transferred to polyvinylidene difluoride membranes (Thermo Fisher Inc., Rockford, IL, USA) and immunoblotted with anti-Bcl-2 (2876), -Bcl-xL (2764), -Mcl-1 (4572), -cleaved-caspase 3 (9661), -caspase 9 (9505), -PARP-1 (9542), -γH2AX (2577), -MEK1/2 (9122), -Bax (2774, Cell Signaling Technology, Danvers, MA, USA), -Histone H4 (07-108, Upstate Biotechnology, Lake Placid, NY, USA) or -β-actin antibody (A2228, Sigma-Aldrich) as described previously (Ge et al., 2006 (link); Ge et al., 2005 (link)). Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li-Cor, Lincoln, NE, USA), as described by the manufacturer. Densitometry measurements were made using Odyssey V3.0 (Li-Cor), normalized to β-actin, and graphed as the fold change compared to the no drug treatment control.
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10

Western Blot Analysis of Cell Signaling

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Cells were lysed in the presence of protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN, U.S.A.). Whole-cell lysates were subjected to SDS-polyacrylamide gel electrophoresis, electrophoretically transferred onto polyvinylidenedifluoride (PVDF) membranes (Thermo Fisher Inc., Rockford, IL, U.S.A.), and immunoblotted with anti-Bcl-2, -Bcl-xL, -Mcl-1, -XIAP, -PARP, -Bim, -Bak, -Bax, -survivin, -γH2AX, -cleaved caspase-3 (designated-cf caspase-3, Cell Signaling Technology, Danvers, MA, U.S.A.), −CHK1, -RAD51 (Santa Cruz), -acetyl-histone 4 (ac-H4), -H4 (Upstate Biotechnology, Lake Placid, NY), -acetyl-tubulin (actubulin), or -β-actin (Sigma-Aldrich) antibody, as previously described. Immunoreactive proteins were visualized using the Odyssey Infrared Imaging System (Li-Cor, Lincoln, NE, U.S.A.), as described by the manufacturer. Western blots were repeated at least three times, and one representative blot is shown. Densitometry measurements were made using Odyssey V3.0 (Li-Cor), normalized to β-actin, and then compared to the corresponding no drug treatment control.
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