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10 protocols using anti mouse alexa fluor 680

1

Quantitative Western Blot Analysis

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The method for cell lysis and Western blotting is described elsewhere [23 (link)]. The primary antibodies used were mouse anti-Mad2 (Abcam, Cambridge, UK, ab10691, 1:500 or 1:1000), mouse anti-securin (Abcam, ab3305, 1:250), mouse anti-cyclin B1 (BD Biosciences, San Jose, CA, USA, 554178, 1:500), mouse anti-GAPDH (Advanced ImmunoChemical Inc., Long Beach, USA, or HyTest Ltd, Turku, Finland, mAb 6C5, 1:30 000-50 000), and mouse anti-E2F1 (Santa Cruz, Dallas, TX, USA, sc-251, 1:500). Secondary antibodies were Alexa Fluor® anti-mouse 680 (Invitrogen), IR Dye® conjugated anti-mouse 800 (Rockland Immunochemicals Inc., Gilbertsville, PA, USA) and HRP-linked anti-mouse IgG (Cell Signaling Technology). Secondary antibodies were used as 1:5000 dilutions with 1 h incubation at RT. The signal measurement and the quantitative analysis were done using a two channel Odyssey Infrared Imaging System (LI-COR Biotechnology) or ECL detection system and ImageQuant LAS4000 CCD camera (Fujifilm, GE Healthcare).
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2

HeLa Cell Protein Extraction and Western Blot

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HeLa cells were centrifuged and washed once with cold PBS before preparation of extract or freezing the pellets in liquid nitrogen. For the preparation of extracts, cells were lysed in 20 mM Tris-HCl (pH 7.7), 100 mM KCl, 50 mM sucrose, 1 mM MgCl2, 0.1 mM CaCl2, 0.5% TX-100 (APC-buffer) containing protease inhibitor cocktail (Roche, 04693132001) and phosphatase inhibitor PhosSTOP (Roche, 4906837001) for 7 min on ice, and cell lysates were cleared by centrifugation. Equal amounts of samples were loaded and run on 4–20% gradient gels followed by semi-dry transfer with Trans-blot (Bio-Rad, Hercules, CA). Membranes were blocked in 5% milk or Odyssey blocking buffer (Fisher Scientific, NC9877369) in TBS for 1 h, followed by primary antibody incubation for 1 h at RT or overnight at +4°C in TBST (TBS containing 0.05% Tween), and secondary antibody for 1 h at RT in TBST. Primary antibodies against Hec1 (Abcam, ab3613), cleaved PARP (Cell Signaling, 9546, dilution) and GAPDH (Advanced ImmunoChemical Inc., mAb 6C5) were followed by secondary antibody Alexa Fluor® anti-mouse 680 (Invitrogen). Signals were detected using Odyssey Infrared Imaging System (LI-COR Biosciences, Lincoln, NE, USA).
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3

Western Blot Protein Detection

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Proteins were separated by SDS-PAGE and transferred to nitrocellulose membranes. The membranes were exposed to antibodies at specific dilutions. Specific protein bands were detected using infrared-emitting conjugated secondary antibodies: anti-mouse 680 Alexa Fluor (Molecular Probes) or anti-rabbit IR Dye 800 (Rockland Immunochemicals), using the Odyssey Infrared Imaging System and the Application software version 2.0 from Li-Cor Biosciences as was previously described [20 (link)]. Blots were quantified by densitometry using GelEval 1.37 software.
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4

Western Blot Protein Detection Protocol

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Western immunoblots were obtained from total protein extracts as described previously [21, 22] . Briefly, treated cells in 6-cm dishes were washed with ice-cold phosphate-buffered saline (PBS) containing 2 mmol/l sodium orthovanadate. Cells were collected by scrapping in 1 ml cold PBS, centrifuged at 13,000 rpm for 5 min at 4 C and the supernatants were discarded. Cells pellets were re-suspended in 50 μl lysis buffer, vortexed, and incubated at 4 C for 30 min followed by centrifugation at 13,000 rpm for 15 min at 4 C. The supernatants were collected, and the concentrations of the supernatant were measured with a BCA protein assay kit (Pierce, Rockford, lL, USA). Proteins were resolved on a 12% SDS-PAGE by loading 25 μg protein and then transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore, (Bedford, MA, USA). The membranes were incubated with blocking buffer (1% casein in PBS) (Bio-Rad, Hercules, CA, USA) for 60 min at room temperature (RT). The membranes were incubated with primary antibody overnight at 4 C. Proteins were visualized using an infrared-emitting conjugated secondary antibodies anti-mouse 680 Alexa Fluor (Molecular Probes, Eugene, OR, USA) or anti-rabbit IRDYE 800 (Rockland Immunochemicals, Gilbertsville, PA, USA) diluted 1:15,000 for 60 min. Band intensities were quantified using Odyssey imaging system (LI-COR Biosciences, Lincoln, NE, USA).
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5

Protein Expression Analysis in Cstb Mutant Mice

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Cerebella of P7 and P30 Cstb−/− and control mice (n = 3 per genotype) were lysed with 50 mM Tris (pH 8.0), 0.5% Nonidet P-40, 10% glycerol, 0.1 mM EDTA, 250 mM NaCl, 0.1 mM Na3VO4, 50 mM NaF, 4 mM dithiothreitol (DTT), 1× Protein inhibitor cocktail (Roche, Basel, Switzerland) using Lysing Matrix D tubes (Qbiogene, Carlsbad, CA, USA) and FastPrep® FP120 Instrument (Qbiogene, Carlsbad, CA, USA). Lysed proteins (15 µg) were separated with Protean TGX precast gels (Bio-Rad Laboratories, Hercules, CA, USA) and transferred on the nitrocellulose membrane. The primary antibodies used were rabbit anti-rat GABRA6 (1∶1000) (Synaptic Systems, Göttingen, Germany) and mouse anti-rat β-tubulin (1∶10 000) (Sigma, St. Louis, MO, USA), and the secondary antibodies used were anti-rabbit-IRDye 800CW (1∶10 000) (LI-COR Biosciences, Lincoln, NE, USA) and anti-mouse-Alexa Fluor 680 (1∶10 000) (Invitrogen®, Life Technologies, Carlsbad, CA, USA). The bands were detected with Odyssey infrared reader (LI-COR Biosciences, Lincoln, NE, USA). Signal intensities were detected with Image Studio 3.1 (LI-COR Biosciences, Lincoln, NE, USA) and normalized to the intensity of β-tubulin.
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6

E3 Auto-Ubiquitylation and Substrate Assays

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For E3 auto-ubiquitylation assays, 1 μM human E1, 5 μM UbcH7, 2 μM E3 (HHARI, Triad1) and 20 μM HA-Ub were incubated at 37 °C in 25 mM HEPES, 100 mM NaCl, 0.5 mM DTT, pH 7.5. Reactions were initiated with 5 mM ATP, 10 mM MgCl2 and quenched with SDS-PAGE reducing buffer. Substrate ubiquitylation assays were performed similarly to auto-ubiquitination, with the addition of 5 μM T7–4EHP. Samples were run on SDS-PAGE gel and visualized on Western blots, blotting for tags on Ub (auto-ubiquitylation) and 4EHP (substrate). Antibodies used were as follows: HA antibody - Bethyl, A190–108A; T7 antibody – Novagen, 69522; Anti-Rabbit DyLight 800, Cell Signaling 5151S; and Anti-Mouse Alexa Fluor 680, Invitrogen, A21058.
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7

Western Blot Analysis of Cellular Proteins

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Whole cell extracts were prepared in 50 mM Tris-HCl, 150 mM NaCl, 1% NP40, 10 mM NaF, 10% Glycerol, supplemented with protease inhibitor cocktail (Roche, Cat. No. 04693116001) and quantitated using a BCA approach. 60 μg of protein, or 40 μl of conditioned media, was run on 10% acrylamide gels and transferred onto nitrocellulose membrane. Western blots were imaged on radiography film or by a LI-COR Odyssey system. actin or vinculin served as loading controls. Primary antibodies: phospho-Akt (Ser473; Cell Signaling Technology, Cat. No. 4060S), pan-Akt, (Life Technologies, Cat. No. 44609G), androgen receptor (Santa Cruz Biotechnology, Cat. No. sc-816), SEMA3C (Santa Cruz Biotechnology, Cat. No. sc-27796), GATA2 (Santa Cruz Biotechnology, Cat. No. sc-9008), FOXA1 (Santa Cruz Biotechnology, Cat. No. sc-6553), POU2F1 (Santa Cruz Biotechnology, Cat. No.s sc-232, sc-8024; Cell Signaling Technology, Cat. No. 4428S), actin (Sigma-Aldrich, Cat. No. A2066), and vinculin (Sigma-Aldrich, Cat. No. V4505). Secondary antibodies: anti-rabbit alexa fluor 680 (Invitrogen, Cat. No. A21109), anti-mouse alexa fluor 680 (Invitrogen, Cat. No. A21058), anti-goat alexa fluor 680 (Invitrogen, Cat. No. A21084), anti-rabbit HRP (Dako, Cat. No. P0448), anti-mouse HRP (Dako, Cat. No. P0447), and anti-goat HRP (Dako, Cat. No. P0160).
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8

Western Blot Protocol for FOXA1 Analysis

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Whole cell extracts were prepared in 50 mM Tris–HCl, 150 mM NaCl, 1% NP40, 10 mM NaF, 10% Glycerol, supplemented with protease inhibitor cocktail (Roche, 04,693,116,001) and quantitated using a BCA approach. 60 µg of protein was run on 10% acrylamide gels and transferred onto nitrocellulose membrane. Western blots were imaged on a LI-COR Odyssey system. Vinculin served as a loading control. Primary antibodies: FOXA1 (Santa Cruz Biotechnology, sc-6553, RRID:AB_2104865) and vinculin (Sigma-Aldrich, V4505, RRID:AB_477617). Secondary antibodies: anti-mouse alexa fluor 680 (Invitrogen, A21058, RRID:AB_2535724), and anti-goat alexa fluor 680 (Invitrogen, A21084, RRID:AB_2535741).
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9

Western Blot Analysis of Prostate Cancer Markers

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Lysis buffer contained 50 mM Tris-HCl, 150 mM NaCl, 1% NP40, 10 mM NaF, 10% Glycerol, and protease inhibitor cocktail (Roche, ON, Canada. Cat. No. 04693116001). Western blots were imaged by a LI-COR Odyssey system. Loading controls were run on the same blots. Primary antibodies include: AR (Santa Cruz Biotechnology, TX, USA. Cat. No. sc-816), PSA (Cell Signaling Technology, MA, USA. Cat. No. 5877), SEMA3C (Santa Cruz Biotechnology Cat. No. sc-27796), AKR1C3 (Abcam, ON, Canada. Cat. No. ab49680), HSD3B2 (Abnova, ON, Canada. Cat. No. 3284-mo2), HSD17B3 (Abnova Cat. No. 29–119), FASN (Cell Signaling Technology. Cat. No. 3180), HMGCS1 (Cell Signaling Technology. Cat. No. 36877), SREBP-1 (Santa Cruz Biotechnology. Cat. No. sc-13551), UGT2B17 (Abcam. Cat. No. ab126269) and actin (Sigma-Aldrich, ON, Canada. Cat. No. A2066). Secondary antibodies were anti-rabbit alexa fluor 680 (Invitrogen, Cat. No. A21109), anti-mouse alexa fluor 680 (Invitrogen, Cat. No. A21058), anti-goat alexa fluor 680 (Invitrogen, Cat. No. A21084).
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10

Western Blot Analysis of Organoid Proteins

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Organoids were harvested from matrigel using ice-cold DPBS w/o Ca2+/Mg2+ and lysed in M-PER Mammalian Protein Extraction Reagent (Thermo Scientific, IL) supplemented with protease inhibitors (Roche) according to the manufacturer’s protocol. Cell lysates were resuspended in 40 μl Laemmli Loading Buffer containing beta-mercaptoethanol (Bio-Rad Laboratories, CA) before western blot analysis. Samples were loaded onto 4–20% Tris-Glycine Gradient Gels (Invitrogen) and run at 80 V, 3.5 hours before transfer to nitrocellulose membranes (Whatman Protran, 0.45 μM) at 105 V, 1.5 hours at 4°C. Membranes were blocked for 1 hour at room temperature using KPL Detector Block Solution (Kirkegaard & Perry Laboratories, Inc.). Membranes were incubated for 16 hours at 4°C with a 1:100 dilution of anti-IκBα antibody (Cell Signaling, #4814), 1:100 dilution of anti-IKKα (Cell Signaling, #2682) or 1:2000 dilution of anti-GAPDH (Millipore, MAB374) antibodies followed by a 1 hour incubation with a 1:1000 dilution anti-mouse Alexa Fluor 680 (Invitrogen). Blots were imaged using a scanning densitometer along with analysis software (Odyssey Infrared Imaging Software System).
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