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22 protocols using anti gfp jl 8

1

Western Blotting of Signaling Proteins

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Proteins were extracted from SK-N-MC cells using SDS sample buffer and boiled at 99°C for 10 min prior to western blotting. Primary antibodies used were anti-NUDT16 (SAB2107004, 1:2,000) from Sigma-Aldrich; anti-p-ATR (2853, 1:1,000), anti-p-ATM (5883, 1:1,000), anti-p-CHK1 (2348, 1:1,000), anti-p-CHK2 (2197, 1:1,000), anti-cleaved caspase 3 (9664, 1:500), and anti-myc (2276, 1:2,000) from Cell Signaling Technology; anti-Dicer (ab14601, 1:2,000), anti-TDP-43 (ab109535, 1:2,000), and anti-β-tubulin (ab6046, 1:2,000) from Abcam; and anti-GFP (JL-8, 1:4,000) from Clontech. Secondary antibodies were goat anti-rabbit (11-035-045, 1:5,000) and goat anti-mouse (115-035-062, 1:5,000) from Jackson ImmunoResearch.
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2

Detecting Cellular Proteins: Rap1, Bqt4, Flag, Cdc2

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For the detection of Rap1, GFP-tagged Bqt4, Flag tag, and Cdc2, we used anti-Rap1 (26 (link)), anti-GFP (JL-8; Clontech, Mountain View, USA), anti-Flag (F3165; Sigma) and anti-PSTAIR (P7962; Sigma), respectively.
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3

Ovary Protein Extraction and Western Blot

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25–35 ovaries from females aged 2–3 days post-eclosion on media supplemented with yeast were homogenized in lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1.25% TritonX-100, 1X protease inhibitor, Roche) and centrifuged at 14000 rpm at 4°C for 5 minutes. Total protein in the supernatant was estimated using the Bradford assay (Biorad) and samples were boiled in an equal volume of 4X SDS sample buffer for 5 minutes. 10–20 μg were loaded on 10% SDS-PAGE gels. Primary antibodies were anti-GFP Jl-8 (Clontech, 1:2000) and mouse anti-tubulin T5168 (Sigma; 1:120,000). Secondary antibodies were HRP conjugated goat anti-mouse (Jackson; 1:1,000 for anti-GFP and 1:60,000 for anti-tubulin) and were detected with ECL Western blotting substrate (Pierce).
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4

Immunoprecipitation of MyD88 and IRAK2

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Cells were plated on 10cm tissue-culture treated dishes and grown to confluency (107 cells/plate overnight). Cells were stimulated with ligand as indicated, then lysed in 700μL of buffer containing 1% NP-40, 50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 10% glycerol and protease/phosphatase inhibitors (Roche). 100 μL of cleared lysate was retained for analysis (input) and remaining 600μL was incubated overnight at 4°C with 1μg anti-MyD88 (R&D sciences) or anti-IRAK2 (ProSci). The following day, 50μL of protein G sepharose (GE healthcare) was added for 1 hour. Alternatively, cleared lysates were incubated with Neutravidin agarose beads (Thermo) for 2 hours. Beads were washed 3× with lysis buffer, then proteins were extracted by adding 50μL 2× Laemmli buffer, electrophoresed and immunoblotted with the indicated antibodies using standard conditions. The following antibodies were used: anti-MyD88 (R&D), anti-IRAK2 (Prosci), anti-HA (3F10, Roche), anti-GFP (JL-8, Clontech) and anti-actin (ac-15, Sigma). Anti-IRAK4 was kindly provided by Shizuo Akira.
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5

Immunoblotting Embryonic and S2 Cell Extracts

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Embryonic extracts for immunoblotting were prepared by resuspending embryos in an equal volume of 2X SDS-PAGE Sample buffer (100 mM Tris–Cl (pH 6.8);4% SDS; 0.2% bromophenol blue; 20% glycerol; 200 mM β-mercaptoethanol) and homogenizing with a pestle in a microfuge tube. To make S2 cell extracts 1 mL of resuspended S2 cells were spun down in a microfuge tube, the media was removed, and the pellet resuspended in an equal volume of 2X SDS PAGE Sample buffer. Samples were boiled for 5 min, spun to clear debris, and 10 μl of the resulting extract run on a 7.5% SDS-PAGE gel, and transferred to a nitrocellulose membrane. To detect the transgenic GFP-tagged Abl proteins we used anti-GFP (JL-8, 1:500 or 1:1000, Clontech). Anti-αTubulin (Sigma, 1:10,000) or anti-Pnut (Developmental studies Hybridoma Bank, 1:30) were used as loading controls. Detection was done using HRP-conjugated anti-mouse IgG secondary antibody (Pierce, 1:50,000), and the ECL plus substrate kit (Pierce).
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6

Protein-Protein Interactions in Gametophores

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For protein–protein interactions in gametophores, total protein extracts from gametophores of PpSHR1-3×Myc#16, PpSHR2-3×Myc#46, Citrine–PpSCR1 PpSHR1-3×Myc#29, and Citrine–PpSCR1 PpSHR2-3×Myc#46 plants were prepared with immunoprecipitation buffer (25 mM Tris-HCl [pH 7.5], 75 mM NaCl, 15 mM MgCl2, 15 mM EGTA, 0.1 mM NP-40, 10 mM NaF, 25 mM β-glycerophosphate, 2 mM sodium o-vanadate, and 1× complete protease inhibitor cocktail [Roche]) and were immunoprecipitated with monoclonal anti-Myc (4A6; Sigma-Aldrich) or anti-GFP (JL-8; Clontech) antibodies. The crude extracts and immunoprecipitates were examined using anti-Myc and anti-GFP antibodies.
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7

Comprehensive Protein Extraction and Analysis

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Total cell lysates were harvested using RIPA buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 1% Nonidet P-40, and 0.25% sodium deoxycholate) with protease inhibitor cocktails (Cat#P8340, Sigma-Aldrich, St. Louis, MO, USA). The antibodies used in this study are described below: anti-GFP (JL-8, Clontech, Mountain View, CA, USA), anti-CPAP (ab221134, Abcam, Danvers, MA, USA), anti-STAT3 (9139, Cell signaling, Danvers, MA, USA), anti-phospho-STAT3/Y705 (9145, Cell Signaling), anti-phospho-p65 (3036, Cell Signaling), anti-p65 (8242, Cell Signaling), anti-cleaved caspase-3 (9661, Cell Signaling), anti-GAPDH (sc32233, Santa Cruz, Dallas, TX) and anti-α-tubulin (DM1A, T6299, Sigma-Aldrich).
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8

Antibody-based Western Blotting and Immunofluorescence

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The following antibodies were used for Western blotting (WB) and IF: anti–γ-tubulin GTU88 (IF), α-tubulin clone DM1A (IF+WB), α-tubulin clone YL 1/2 (IF), β-actin clone AC15 (IF), GFP (WB), PPP1R13L HPA041231 (WB), myosin 1c HPA 001768 (IF, WB), FLAG M2 (WB) from Sigma-Aldrich; anti-mCherry (WB) and NuMA [EP3976] (WB) from Abcam; anti-iASPP 18590–1-AP (WB) from Proteintech and PCRP-PPP1R13L-2G4 (WB) from Developmental Studies Hybridoma Bank; anti–ERM #3142 (WB), anti-EB1 clone 5 (WB), and anti-HA clone 6E2 (WB) from Cell Signaling Technology; anti-EB1 KT51 (IF), myosin Ic (13; WB), PP1α (C-19; WB) from Santa Cruz Biotechnology; anti-CDK5RAP2, A300-554 (IF) from Bethyl; anti–Phospho-Histone H3 (Ser10) from Millipore (WB); and anti-GFP JL-8 from Clontech (for GFP1-10, WB). GFP-Trap was from Chromotek, anti-HA agarose conjugated beads, tetramethylrhodamine isothiocyanate (TRITC)-phalloidin from Sigma-Aldrich, and Strep-Tactin beads from IBA.
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9

Immunoprecipitation Protocol for Detecting Protein Interactions

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Cells were collected in lysis buffer (150 mM NaCl, 30 mM Tris, pH 7.5, 1 mM EDTA, 1% TritonX-100, 10% glycerol, 0.5 mM dithiothreitol, and 0.1 mM phenylmethylsulfonyl fluoride, plus proteinase/phosphatase inhibitors [EDTA-free, Thermo Scientific] as in Li et al., 2012 (link)) approximately 24 h after transfection. Antibody was added and samples were incubated on a nutator overnight at 4°C. The next day, Protein A-Sepharose beads (Sigma) were added and samples were incubated on a nutator for 2 h at 4°C. After washing in lysis buffer, immunoprecipitated proteins were removed from the beads with 2× SDS buffer and run on an 8 or 10% SDS–PAGE gel and transferred to a nitrocellulose membrane. Westerns were visualized using x-ray film or the Typhoon Imager. Primary antibodies were: anti-GFP (JL-8; Clontech, 1:1000), anti-Flag (Sigma-Aldrich, 1:2000), and anti-γ-tubulin (Sigma-Aldrich, 1:2000). Secondary antibodies were: IRDye800CW anti-mouse (Licor 1:10,000); HRP–conjugated anti-mouse (Sigma 1:1000).
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10

Immunofluorescence Microscopy Antibodies

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Rabbit anti-Ror2 61 (link) and anti-IFT20 31 (link) antibodies were prepared as described previously. Sheep anti-TGN46 and rabbit anti-Giantin antibodies have been described previously62 (link). Following antibodies were purchased commercially: mouse anti-GM130 (35, BD), anti-Cortactin (4F11, Millipore), anti-γ-tubulin (GTU-88, Sigma), anti-tyrosinated tubulin (TUB01A2, Sigma), anti-AKAP450 (15, BD), anti-GFP (JL-8, Clontech), anti-acetylated tubulin (6-11B-1, Sigma), anti-Myc (9E10, Santa Cruz), anti-Golgin-97 (CDF4, Thermo), and Alexa Fluor 647-conjugated anti-GM130 (5G8, MBL); rabbit anti-IFT20 (13615-1-AP, Proteintech), anti-Arl13B (ab83879, Abcam), anti-GM130 (PM061, MBL), anti-γ-tubulin (T5192, Sigma), anti-Golgin-97 (D8P2K, Cell Signaling Technology), and HRP-conjugated anti-α-tubulin (PM054-7, MBL).
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