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27 protocols using anti bcl 2

1

Antibody Reagents for Cell Signaling

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Anti-LC3B, anti-Bcl-xL, anti-Atg16L1, anti-Rac1, anti-Rho1, anti-Cdc42, anti-phospho-ERK, anti-EEA1 and anti-LAMP1 antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA). Mouse monoclonal antibodies reactive with LRP1 (11H4) were a kind gift from Dr. Strickland, University of Maryland School of Medicine, Baltimore. Fibronectin (EP5) and ubiquitin (P4D1) were from Santa Cruz Biotechnologies (Santa Cruz, CA, USA); anti-Cx43, anti-ERK, anti-Bcl-2 and anti-RPTPβ antibodies were from BD Biosciences (Tokyo, Japan); anti-multi ubiquitin monoclonal antibody (FK1) was from MBL (Nagoya, Japan); anti-GAPDH antibody was from GeneTex (Irvine, CA, USA) and anti-LC3 (clone 1703) antibody was from Cosmo Bio (Tokyo, Japan). Anti-RPTPα rabbit polyclonal antibodies for immunoblotting were provided by Dr. Jan Sap; anti-α-tubulin and anti-FLAG M2 antibodies, N-acetyl-l-cysteine (NAC) and ammonium chloride were from Sigma Aldrich (St. Louis, MO, USA); ProLong Gold Antifade Reagent with DAPI and DIDS were from Invitrogen (Eugene, OR, USA); an ERK inhibitor, U0126, was from Cayman Chemical (Ann Arbor, MI, USA); Rac1 inhibitor, NSC23766 was from Wako Pure Chemical Industries (Osaka, Japan); and GSH was from Merck (Darmstadt, Germany).
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2

Western Blot Analysis of Apoptosis Regulators

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Thymocyte lysates were prepared using RIPA buffer (300 mM NaCl, 2% octylphenoxypolyethoxyethanol (IGEPAL CA-630; Sigma-Aldrich), 1% deoxycholic acid, 0.2% SDS, 100 mM Tris-HCl pH 8.0) containing protease inhibitors (Roche, Basel, Switzerland) and platelet lysates with NP40 lysis buffer (1% octylphenoxypolyethoxyethanol, 150 mM NaCl, 50 mM Tris-HCl, pH 7.4) containing protease inhibitors. Proteins were separated on NuPAGE Bis-Tris gels (Life Technologies, Carlsbad, CA, USA) according to manufacturer's instructions. Blots were probed with: anti-Mcl-1 (clone 19C4-15; WEHI mAb facility), anti-human Bcl-2 (clone Bcl-2-100;46 (link) WEHI mAb facility), anti-Bcl-2 (clone 7; BD Biosciences), anti-Bim (polyclonal; Enzo Lifesciences, Farmingdale, NY, USA), anti-Bcl-xL (polyclonal; BD Biosciences), anti-Bak (polyclonal; Sigma-Aldrich) and anti-β-actin (clone AC-74; Sigma-Aldrich).
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3

Western Blot Analysis of Larval Responses

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At each time point, 30 larvae from control or metronidazole treatment groups were harvested in RIPA lysis buffer containing 1 mM phenylmethanesulfonyl fluoride (PMSF; Sigma, 78830), Protease Inhibitor Cocktail (Promega, G6521), Phosphatase Inhibitor Cocktail 2 (Sigma, P5726), and Phosphatase Inhibitor Cocktail 3 (Sigma, P0044). Western blotting was performed using standard protocols [48 (link)]. Eleven primary antibodies were used in this study: anti-IL-7R (1:1500; Abcam, ab180521), anti-MBP (1:500; Anaspec, #55811, Fermont, CA, USA), anti-Phospho-JAK1 (1:1,000; Cell Signaling Technology, #3331, Danvers, MA, USA), anti-Phospho-JAK3 (1:500; Cell Signaling Technology, #5031), anti-STAT3 (1:500; Santa Cruz Biotechnology, sc-7179, TX, USA), anti-Phospho-STAT3 (1:200; Cell Signaling Technology, #9145), anti-STAT5 (1:500; Santa Cruz Biotechnology, sc-836), anti-Phospho-STAT5 (1:200; Cell Signaling Technology, #9351), anti-BCL2 (1:1000; BD Biosciences, 610538), anti-CASPASE-3/cleaved CASPASE-3 (1:300; Wanleibio, WL02117), and anti-CASPASE-7/cleaved CASPASE-7 (1:500; Wanleibio, WL0181). Anti-glyceraldehyde-3-phosphate dehydrogenase (anti-GAPDH; 1:3,000; Millipore, MAB374, Billerica, MA, USA) was used as a loading control.
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4

Apoptotic Signaling Pathway Analysis

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All cell culture and transfection reagents were from Invitrogen; and standard reagents were from Sigma or Fisher Scientific. Drugs were from: ABT-737 (Abbott Pharmaceuticals), ABT-263/PLX-4032/GSK-110212 (Selleck), zVAD-fmk (Calbiochem), Hoechst 33342 (Anaspec), and staurosporine/cisplatin/dacarbazine/vinblastine (Sigma). Antibodies (clone): anti-actin (C4), anti-A1 (FL-175), anti-BCL-2 (100), anti-CD31 (BD Pharmingen #550274) anti-MCL-1 (Rockland), anti-BAD (C7), anti-BIM (22 (link)–40), anti-PUMA (CT; Sigma), anti-SMAC (H177), anti-BID (C20), anti-cytochrome c (7H8.2C12), anti-BAK (G23), anti-BAX (6A7 for IP; N20 for western blot), anti-BCL-xL (H5 for IP; S18 for western blot), anti-GAPDH (9B3), anti-HSP60 (B-9), anti-p44/p42 MAPK ERK1/2 (137F5), and anti-phospho p44/42 MAPK ERK1/2 (197G2). Caspase-8 cleaved mouse BID (C8-BID) was from R&D Systems. Full-length BAX was made as described (24 (link)). Human BCL-xLΔC, MCL-1ΔC, and PUMAβ were made as described (17 (link)). The human BIM BH3 domain peptide (> 98% purity, Abgent) was resuspended in anhydrous DMSO in a N2 environment, stored at −80°C, and thawed only once. All lipids for the LUVs studies were purchased from Avanti Polar Lipids. Statistical significance was evaluated by two tailed Student t test for p < 0.05.
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5

Histological and Immunohistochemical Analysis of Mouse Organs

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Histological analysis of mouse organs was performed on 4 μm thick FFPE tissue sections, stained with Hematoxylin & Eosin (H&E) (Thermo Scientific)53 (link). The following primary antibodies and dilutions were used for immunohistochemical analysis: rabbit polyclonal anti-Bcl6 (1:300) (N3, Santa Cruz Biotechnology) and anti-Pax5 (1:400) (Neomarker); rabbit monoclonal anti-CD3 (1:800) (clone SP7, Neomarker) and anti-Ki67 (1:200) (clone SP6, Thermo Scientific); rat monoclonal anti-B220 (1:400) (clone RA3-6B2, BD Biosciences) and anti-CD138 (1:200) (clone 281-2, BD Biosciences); mouse monoclonal anti-BCL2 (1:200) (clone Bcl-2/100, BD Biosciences).
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6

Western Blot Analysis of Signaling Proteins

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Primary antibodies used in this study were purchased from Cell Signaling Technology (Beverly, MA): anti-pPKAThr198/PKA, anti-pCREBSer133/CREB, anti-pSTAT3Tyr705/STAT3, anti-pSrcSer17/Src, anti-pACC Ser79/ACC, anti-pAktSer473/Akt, anti-pAMPK Thr172/AMPK, anti-p4EBP1Thr37/46/4EBP1, anti-pmTORSer2448/mTOR, anti-pP70S6KThr389/P70S6K, anti-EPAC-1, anti-BEATA2_AR, anti-FAK, anti-FASN, anti-GLUT4, anti-OCT3, anti-NOTCH, anti-PGC1, anti-pPRAS40Thr246, anti-PRAS40, anti-pRAPTORSer792, anti-RAPTOR, and anti-PI3K110α. Anti-BCL-2 was purchased from BD Bioscience (San Jose, CA). Anti-P27 was purchased from Thermo Fisher Scientific (Waltham, MA). Anti-rabbit immunoglobulin-horseradish peroxidase-conjugated secondary antibody, LumiGLO reagent with peroxide and cAMP assay kit were also purchased from Cell Signaling Technology, Inc. (Beverly, MA). Anti-IGF1Rα, anti-HMGCR, anti-P21, anti-SCD1, and anti-SCEBP1 were obtained from Santa Cruz Biotechnology, Inc. (Dallas, TX); mouse anti-β-actin primary antibody was obtained from Sigma Aldrich (St. Louis, MO). The 1-methyl-1-nitrosourea (MNU) was obtained from Ash Stevens (Detroit, MI) and stored at −80°C prior to use. Metformin and buformin were obtained from Waco Pure Chemical Industries, (Waco, TX); phenformin was obtained from Sigma Aldrich (St. Louis, MO).
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7

Antibody Profiling for Cell Stress Signaling

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The following antibodies were used in the study: anti-GRP78 (sc-1050, Santa Cruz, CA, USA), anti-p-PERK Thr981 (sc-32577, Santa Cruz), anti-eIf2α (sc-133132, Santa Cruz), anti-CRT (sc-166837, Santa Cruz), anti-ERp57 (sc-28823, Santa Cruz), anti-Ub (sc-8017, Santa Cruz), anti-p-Akt1/2/3 (sc-7985, Santa Cruz), anti-GAPDH (sc-32233, Santa Cruz), anti-GFP (sc-8334, Santa Cruz), anti-Lamin B1 (sc-374015, Santa Cruz), anti-CaM (sc-137079, Santa Cruz), anti-CaMKIIγ (sc-1541, Santa Cruz), CREB-1 (sc-186, Santa Cruz), anti-p-CaMKII (ab182647, abcam, Waltham, MA, USA), anti-Bcl-2 (610539, BD Biosciences, Franklin Lakes, NJ, USA), anti-cleaved-caspase 3 (9664, Cell Signaling Technology, Danvers, MA, USA), anti-p-CREB Ser133 (9198, Cell Signaling Technology), anti-p-eIF2α Ser51 (9721, Cell Signaling Technology), and anti-PARP (9542, Cell Signaling Technology). All secondary antibodies (HRP-conjugated anti-rabbit, anti-mouse, and anti-goat) were purchased from Sigma (Sigma-Aldrich Inc., St. Louis, MO, USA). All the drug formulations were purchased from Sigma (Sigma-Aldrich Inc.).
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8

Histological and Immunohistochemical Analysis of Mouse Organs

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Histological analysis of mouse organs was performed on 4 μm thick FFPE tissue sections, stained with Hematoxylin & Eosin (H&E) (Thermo Scientific)53 (link). The following primary antibodies and dilutions were used for immunohistochemical analysis: rabbit polyclonal anti-Bcl6 (1:300) (N3, Santa Cruz Biotechnology) and anti-Pax5 (1:400) (Neomarker); rabbit monoclonal anti-CD3 (1:800) (clone SP7, Neomarker) and anti-Ki67 (1:200) (clone SP6, Thermo Scientific); rat monoclonal anti-B220 (1:400) (clone RA3-6B2, BD Biosciences) and anti-CD138 (1:200) (clone 281-2, BD Biosciences); mouse monoclonal anti-BCL2 (1:200) (clone Bcl-2/100, BD Biosciences).
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9

Apoptotic Signaling Pathway Analysis

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All cell culture and transfection reagents were from Invitrogen; and standard reagents were from Sigma or Fisher Scientific. Drugs were from: ABT-737 (Abbott Pharmaceuticals), ABT-263/PLX-4032/GSK-110212 (Selleck), zVAD-fmk (Calbiochem), Hoechst 33342 (Anaspec), and staurosporine/cisplatin/dacarbazine/vinblastine (Sigma). Antibodies (clone): anti-actin (C4), anti-A1 (FL-175), anti-BCL-2 (100), anti-CD31 (BD Pharmingen #550274) anti-MCL-1 (Rockland), anti-BAD (C7), anti-BIM (22 (link)–40), anti-PUMA (CT; Sigma), anti-SMAC (H177), anti-BID (C20), anti-cytochrome c (7H8.2C12), anti-BAK (G23), anti-BAX (6A7 for IP; N20 for western blot), anti-BCL-xL (H5 for IP; S18 for western blot), anti-GAPDH (9B3), anti-HSP60 (B-9), anti-p44/p42 MAPK ERK1/2 (137F5), and anti-phospho p44/42 MAPK ERK1/2 (197G2). Caspase-8 cleaved mouse BID (C8-BID) was from R&D Systems. Full-length BAX was made as described (24 (link)). Human BCL-xLΔC, MCL-1ΔC, and PUMAβ were made as described (17 (link)). The human BIM BH3 domain peptide (> 98% purity, Abgent) was resuspended in anhydrous DMSO in a N2 environment, stored at −80°C, and thawed only once. All lipids for the LUVs studies were purchased from Avanti Polar Lipids. Statistical significance was evaluated by two tailed Student t test for p < 0.05.
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10

Protein Expression Analysis Methodology

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Protein expression was assessed as previously described (19 (link)). Antibodies used were: anti-MCL-1 (Rockland Immunochemical, PA), anti-human MCL-1, anti-PARP, anti-CHOP, and anti-BCL-XL (Cell Signaling, MA). Anti-BCL-2 (BD Biosciences, CA), anti-NOXA and anti-PUMA (Sigma Aldrich, MO), and anti-Actin (Millipore, MA). Anti-rabbit or anti-mouse horseradish peroxidase-conjugated secondary antibodies were from Jackson Immunochemical, ME. Immunoblots were acquired on a LI-COR Odyssey (LI-COR, NB) and densitometry assessed for all blots in replicate for statistical analysis (Sup. Fig. 7).
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