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15 protocols using α myc

1

Immunoprecipitation and Western Blot Analysis of Hearing-related Proteins

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DNA constructs are described in Supplementary Information. Expression of the constructs, immunoprecipitations, and Western blots were carried out as described (Senften et al., 2006 (link)). Immunoprecipitation experiments were carried out at least 3 times to verify the reproducibility of the data. The following antibodies were used for the experiments: α-TMIE (rabbit, Sigma); α-HA (mouse, Cell signaling); α-Myc (rabbit, Cell signaling); α-Flag (rabbit, Sigma); α-GFP (Wei et al., 2012); α-PCDH15 (Kazmierczak et al., 2007 (link)); α-LHFPL5 (Longo-Guess et al., 2005 (link)).
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2

Immunoprecipitation of Fam65b Complexes

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DNA constructs are described in Supplementary Information. Expression of the constructs, immunoprecipitations, and western blots were carried out as described (Senften et al., 2006 (link)). Immunoprecipitation experiments were carried out at least 3 times to verify the reproducibility of the data. The following antibodies were used for the experiments: α- Fam65b (rabbit, Sigma); α-HA (mouse, Cell signaling); α-Myc (rabbit, Cell signaling); α-GFP (Xiong et al., 2012 (link)); α-GFP (mouse, Santa Cruz).
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3

Characterization of Immune Signaling Pathways

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Western blotting and immunoprecipitations were performed as described (Ho et al., 2010 (link); Maitra et al., 2007 (link)). Antibodies: α-A20, α-myc and α-IκBζ from Cell Signaling; α-MCPIP1, α-TRAF6, α-Act1 from Santa Cruz Biotechnology; α-HA, α-FLAG from Sigma. Blots were developed with a FluorChem E imager (Protein Simple, Santa Clara CA). Abs against IL-17RA were from Amgen (clone M751). ELISA kits were from eBioscience (San Diego, CA). Histology was performed by the University at Buffalo Histology Core (Buffalo, NY) and imaged on an EVOS FL microscope system (Life Technologies). For flow cytometry, CNS cells were stained with Abs from eBioscience or BD and analyzed on a FACS Fortessa with FlowJo (Tree Star).
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4

Immunofluorescence analysis of autophagy proteins

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HEK293T, HeLa, or MEF cells were grown in chamber slides (Thermo Fisher), or on cover slips (Chemglass) in 24-well plates, and transfected and/or infected as indicated. Cells were fixed with 4% (w/v) paraformaldehyde (PFA, Santa Cruz) for 20 min, permeabilized with 0.5% (v/v) Triton-X-100 in PBS, and then blocked with 10% (v/v) goat serum or 1% milk powder in PBS for 1 h. For immunostaining, α-TRIM23 (1:200, ab97291, Abcam), α-LC3 (1:400, Novus Biologicals), α-phospho-S172-TBK1 (1:400, 5483, Cell Signaling), α-TBK1 (1:400, #3013, Cell Signaling), α-TRIM23 (1:100, clone C-1, sc-393923, Santa Cruz), α-FLAG (1:400, M2, Sigma), α-p62 (1:400, PROGEN Biotechnik), α-LAMP1 (1:400, H4A3, Developmental Studies Hybridoma Bank), α-V5 (1:500, R960-25, Life Technologies), α-myc (1:400, 9B11, Cell Signaling) and α-ATG16 (1:200, A7356, Sigma) were used, followed by incubation with secondary antibodies conjugated to Alexa Fluor 488, Alexa Fluor 555, Alexa Fluor 594, Alexa Fluor 633, or Alexa Fluor 647 (all 1:400, Life Technologies). Cells were mounted in DAPI-containing Vectashield (Vector Labs) to co-stain nuclei. All laser scanning images were acquired on an Olympus IX8I confocal microscope or on a Leica SP8 confocal microscope. Cytoplasmic GFP-LC3B puncta in HeLa, HEK293T and MEF cells were manually counted for 30 or 50 randomly selected cells.
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5

Protein Extraction and Western Blotting Protocol

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From cultures in mid-log phase, cell pellets of equivalent optical densities were collected, washed with 1 ml 4°C H2O, and frozen on dry ice. Pellets were thawed in boiling sample buffer (50 mM Tris pH 7.5, 5% SDS, 5 mM EDTA, 10% glycerol, 0.5% β-mercaptoethanol, bromophenol blue, 1 μg/ml leupeptin, 1 μg/ml bestatin, 0.1 mM benzamidine, 1 μg/ml pepstatin A, 5 mM NaF, 1 mM Na3VO4, 80 mM β-glycerophosphate, 1 mM phenylmethylsulfonyl fluoride). Cells were boiled for 3 minutes, bead-beaten with glass beads for 3 minutes, and clarified by centrifugation. Extracts were analyzed by SDS-PAGE and Western blotting. Western blots were performed with low-salt phosphate buffered saline with Tween-20 (PBS-T) (15 mM NaCl, 1.3 mM NaH2PO4, 5.4 mM Na2HPO4, 0.05% Tween-20). Primary antibody incubations were performed in 5% nonfat dry milk and low salt PBS-T. Antibodies were used as follows: α-ilk and low salt PBS-T. Antibodies were used as follows:α-ilk and low salt PBS-T. Antibodies were used asαilk and low salt PBS-T. Antibodies were used as for α-Myc (9E10), α-Myc (9E10), saltD. Kellogg), and α-phospho-Cdc2 (Y15) (antibody was raised against human Cdc2 but recognizes S. cerevisiaie Cdc28 inhibitory phosphorylation as well, from Cell Signaling Technology #9111).
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6

Antibody Sources for Western Blot Analysis

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Antibodies were obtained from the following sources: α-myc (Cell Signaling, Inc., Beverly, MA. Catalog number: 2272), α-hemagglutinin (HA) (Roche Applied Science, Indianapolis, IN. Catalog number: 11867423001), α-NFATc1 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA. Catalog number: sc-7294), α-Mitf (C5) (Calbiochem, San Diego, CA. Catalog number: MAB3747-I and a gift from Dr. David E. Fisher at Massachusetts General Hospital, Boston, MA) and α-tubulin (Sigma-Aldrich, St. Louis, MO. Catalog number: T9026-100UL). Cyclosporine A (CsA), polyinosinic-polycytidylic acid and SigmaFAST protease inhibitor were purchased from Sigma-Aldrich. Recombinant murine M-CSF and RANKL were purchased from PeproTech (Rocky Hill, NJ). All primers and probes were purchased from Integrated DNA technologies (Coralville, IA).
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7

Immunostaining of HEK293 Cells and Cochlear Whole Mounts

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Cochlear whole mount staining and immunocytochemistry of HEK293 cells were carried out as described (Xiong et al., 2012 (link)). Primary antibodies were as follows: α-TMIE (rabbit, Sigma); α-HA (mouse, Cell signaling); α-Myc (rabbit, Cell signaling). Additional reagents were: Alexa Fluor 488-phalloidin, Alexa Fluor 594 goat anti-rabbit, TOP-RO3 and Alexa Fluor 647-phalloidin (Invitrogen, Carlsbad, CA).
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8

Immunoblot Analysis of Parasite Proteins

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To prepare samples of the total extracts, parasites were purified by filtering through 3μm polycarbonate filters (EMD Millipore), washed in PBS, re-suspended with Leammli loading dye and lysed at 65°C for 10 min. To analyze individual fractions after immunoprecipitation, an aliquot of the fraction was mixed with Leammli loading dye and heated for 10 min at 65°C. After separation on SDS-PAGE gels, proteins were transferred onto a nitrocellulose membrane and probed with monoclonal α-HA (3F10, Roche Applied Sciences), α-myc (Cell Signaling Technology) and α-Tubulin A (12G10, kindly provided by Dr. Jacek Gaertig, University of Georgia) antibodies. After incubation with secondary HRP-conjugated antibodies, proteins were visualized by enhanced chemiluminescence detection (PerkinElmer).
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9

Immunofluorescence analysis of autophagy proteins

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HEK293T, HeLa, or MEF cells were grown in chamber slides (Thermo Fisher), or on cover slips (Chemglass) in 24-well plates, and transfected and/or infected as indicated. Cells were fixed with 4% (w/v) paraformaldehyde (PFA, Santa Cruz) for 20 min, permeabilized with 0.5% (v/v) Triton-X-100 in PBS, and then blocked with 10% (v/v) goat serum or 1% milk powder in PBS for 1 h. For immunostaining, α-TRIM23 (1:200, ab97291, Abcam), α-LC3 (1:400, Novus Biologicals), α-phospho-S172-TBK1 (1:400, 5483, Cell Signaling), α-TBK1 (1:400, #3013, Cell Signaling), α-TRIM23 (1:100, clone C-1, sc-393923, Santa Cruz), α-FLAG (1:400, M2, Sigma), α-p62 (1:400, PROGEN Biotechnik), α-LAMP1 (1:400, H4A3, Developmental Studies Hybridoma Bank), α-V5 (1:500, R960-25, Life Technologies), α-myc (1:400, 9B11, Cell Signaling) and α-ATG16 (1:200, A7356, Sigma) were used, followed by incubation with secondary antibodies conjugated to Alexa Fluor 488, Alexa Fluor 555, Alexa Fluor 594, Alexa Fluor 633, or Alexa Fluor 647 (all 1:400, Life Technologies). Cells were mounted in DAPI-containing Vectashield (Vector Labs) to co-stain nuclei. All laser scanning images were acquired on an Olympus IX8I confocal microscope or on a Leica SP8 confocal microscope. Cytoplasmic GFP-LC3B puncta in HeLa, HEK293T and MEF cells were manually counted for 30 or 50 randomly selected cells.
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10

Immunocytochemistry of Neuronal Cultures

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Primary neuronal cultures were fixed in 3.6% PFA in PBS for 10 minutes at room temperature. Neurons were then permealized in 0.25% PBST for 15 minutes at room temperature and blocked in 1% BSA in PBST for 1 h at room temperature, incubated with primary antibodies at 4 °C overnight, secondary antibodies at room temperature for 1 h and mounted with anti-DAPI prolong-gold anti-fade mounting media (Invitrogen). Neurons were washed with PBS three times between each step. The following primary antibodies were used: α-C9ORF72 (Sigma#HPA023873, 1:200), α-Myc (Cell Signaling#2276, 1:1,000), α-TIAR (BD Transduction Laboratories#610352, 1:250), α-DCP1A (Sigma#D5444, 1:500), α-Nucleolin (ProteinTech#10556-1-AP, 1:2,000), α-SMI32 (Covance#SMI-32R, 1:1,000), α-MAP2 (Millipore#AB5622, 1:500), α-Fibrillarin (SantaCruz#sc-25397, 1:200) α-TU20 (Abcam#ab7751 1:500), α-HB9 (DSHB#81.5C10, 1:5), α-Tuj1 (Millipore#AB9354, 1:1,000), α-PR (ProteinTech#23979-1-AP, 1:1,000). Cells were imaged using confocal microscopy (Olympus FV1000). 6–10 images at a 0.3 μm step-size were acquired and projected onto one single image.
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