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15 protocols using anti c myc

1

Quantitative Worm Protein Analysis

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Approximately 400 L4 worms were collected in M9 buffer and snap frozen in dry ice. Pellets were resuspended in 50 mM Tris, pH 7.5, containing protease inhibitors (Roche). Ceramic beads were added, and worms were lysed using a Precellys 24 homogenizer (Bertin Technologies). Extracts were resolved by SDS-PAGE and transferred to nitrocellulose membrane. Western blot analysis was performed using anti-c-myc (Roche) and anti-α-tubulin (Sigma) primary antibodies. The band intensity was quantified using ImageJ (https://imagej.nih.gov/ij/).
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2

Generating Polyclonal Anti-Shank3a Antibody

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A novel polyclonal antibody directed against the rat Shank3a N-terminus (aa 333-470) was generated for this study according to the antibody production and purification protocol described in [31 (link)]. The anti-Shank3 PRC antibody has been described previously [31 (link)]. The following primary antibodies were purchased from commercial suppliers: anti-histone H3 (Cell Signaling Technology, Danvers, MA, USA), anti-green fluorescent protein (GFP) (Clontech, Laboratories, Mountain View, CA, USA), anti-c-Myc (Roche Applied Science, Mannheim, Germany), as well as anti-GAPDH, anti-VGLUT1, and anti-VGAT (all from Synaptic Systems, Goettingen, Germany).
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3

Comprehensive Purine Biosynthesis Pathway Examination

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Primary antibodies: anti-IMPDH1 (WH0003614M1, dilution 1:200) antibody (Sigma-Aldrich); anti-IMPDH2 (ab131158, dilution 1:400) antibodies (Abcam); anti-GFP (11814460001, dilution 1:1000) antibody (Roche); anti-c-Myc (sc-789, dilution 1:400), anti-c-Myc (sc-40, dilution 1:400), anti-nm23-H1 (sc-465, dilution 1:400) antibodies (Santa Cruz Biotechnology); and anti-GAPDH (#5174, dilution 1:400) antibody (Cell Signaling Technology). Secondary antibodies: goat anti-mouse IgG Alexa 488 (#A-11029), goat anti-rabbit IgG Alexa 568 (#A-11011), and goat anti-rabbit IgG Alexa 488 (#A-11034) antibodies (Invitrogen); Alexa Fluor 546 phalloidin (#A-12380, dilution 1:200) probe (Invitrogen); and DAPI. Plasmids: PRPS1-Myc-DDK (#RC200698), GUK1-Myc-DDK (#RC202510), Atic-Myc-DDK (#MR219425), ADK-Myc-DDK (#RC200628), APRT-Myc-DDK (#RC216874), HPRT1-Myc-DDK (#RC200462), Pnp-Myc-DDK (#MR203940), Ampd1-Myc-DDK (#MR220907), Nt5c1a-Myc-DDK (#MR217369), GAPDH-Myc-DDK (#MR204932) were purchased from OriGene; FGAMS-EGFP (#99107), PAICS-EGFP (#99108), GFP-ATIC (#99110), PPAT-EGFP (#99105), ADSL-EGFP (#99109), ADSS-V5 (#98316) were purchased from Addgene. Rat GMPS (rGMPS) and mCherry were amplified using standard PCR procedures and combined into the pTRIPZ vector using the Gibson assembly cloning kit (New England Biolabs #E5510S).
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4

Yeast Mitochondrial Protein Analysis

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Yeast cells were grown in raffinose medium until late log phase. Mitochondria were isolated as previously described.73 (link) Proteins were separated by SDS-PAGE.74 (link) For western blotting, proteins were transferred to polyvinylidene difluoride (PVDF) membranes and probed with anti-Cox1 (Rodolfo García-Villegas), anti-hemagglutinin (HA) (Roche), anti c-MYC (Roche), anti-citrate synthase (Thomas D. Fox), or anti-cytochrome c1 (Diego González-Halphen and Miriam Vázquez- Acevedo) antibodies. Immune complexes were detected with either goat anti-rabbit immunoglobulin (IgG) or anti-mouse IgG conjugated to horseradish peroxidase (Invitrogen) and the enhanced chemiluminescence kit (Pierce), with the exception that the anti-HA signal was detected using the Immobilion substrate (Millipore) or WestPico Kit (Pierce). Mitochondrial translation products were radiolabeled with 35S methionine in whole cells in the presence of cycloheximide or in purified mitochondria as previously described.75 (link) Mitochondrial separation into membrane and soluble fractions and alkaline carbonate extractions of membranes was as described.35 (link),73 (link)
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5

Antibody Characterization for Cellular Signaling

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Antibodies against Sig1R(L20) (1:250, Cat# sc‐16203), CYPOR(H‐300) (1:250, Cat# sc‐13984) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA). Anti‐IP3R3 (1:1,000, Cat# 610313) antibody was obtained from BD biosciences (San Jose, CA). Anti‐human SOD1 antibody was raised and purified in our laboratory (Bruijn et al, 1997). We also purchased the following commercially available antibodies: anti‐IP3R1 (L24/18) (1:500, Cat# 817701) (BioLegend, San Diego, CA), anti‐FLAG M2 (1:1,000, Cat# F3165) (Sigma‐Aldrich, St. Louis, MO), anti‐c‐myc (1:400, Cat# 11 667 149 001), anti‐influenza hemagglutinin (HA) (1:1,000, Cat# 11 867 423 001) (both from Roche, Basel, Switzerland), anti‐histone H3 (1:1,000, Cat# 9715), anti‐calreticulin (1:500, Cat# 2891), anti‐PDI (1:1,000, Cat# 2446), anti‐VDAC (1:1,000, Cat# 4661) (Cell Signaling Technology, Danvers, MA), anti‐βIII‐tubulin (1:5,000, Cat# PRB‐435P) (Covance, Princeton, NJ), and anti‐spectrin α II (1:500, Cat# MB1622) (EMD Millipore, Billerica, MA). Alexa‐conjugated secondary antibodies (1:1,000) were purchased from Life Technologies (Grand Island, NY), and horseradish peroxidase (HRP)‐conjugated secondary antibodies (1:5,000) were from GE Healthcare (Waukesha, WI).
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6

Protein Expression Analysis by SDS-PAGE and Western Blot

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Standard sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blot analysis was performed. Primary antibodies used were anti-cyclin A1 (BD Biosciences, San Diego, CA, USA), anti-cyclin A2 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-c-MYC (Roche Diagnostics, Indianapolis, IN, USA) and anti-beta-actin (Sigma-Aldrich, Natick, MA, USA). Peroxidase-based pico-chemiluminescence kit (Thermo Fisher Scientific, MA, USA) was used to reveal antibody signal.
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7

Western Blot Protein Detection Protocol

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Total protein extracts were obtained by using the alkali method (34 (link)). Equivalent amounts of protein were resolved on SDS-polyacrylamide gels and transferred to nitrocellulose membranes. Ponceau S staining was used to assess protein transfer and loading. The Flag epitope was detected using a horseradish peroxidase (HRP)-conjugated antibody. The primary antibodies used in this study included anti-Flag (Merck), anti-c-myc (Roche Applied Science), anti-Pgk1 (Thermo Fisher Scientific), anti-glutathione S-transferase (anti-GST) (Merck), and anti-peroxidase-antiperoxidase (anti-PAP) (Merck). Immunoblots were developed with horseradish peroxidase (HRP)-labeled secondary antibodies and the ECL Select Western blotting detection kit (GE Healthcare Life Sciences). Images were scanned with an ImageQuant LAS 4000 mini biomolecular imager (GE Healthcare Life Sciences), and specific signals were quantified and processed with ImageQuant TL analysis software (GE Healthcare Life Sciences).
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8

Western Blot Analysis of Protein Expression

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Proteins were separated by SDS-PAGE and transferred to nitrocellulose membranes (GE Healthcare, 10600003). Membranes were incubated with primary antibodies and secondary antibodies sequentially. Primary antibodies we used include anti-GFP (Roche, 11814460001, 1:5000 dilution), anti-c-myc (Roche, 11667203001, 1:2000 dilution), anti-Flag M2 (Sigma, F1804, 1:5000 dilution), anti-HA (Roche, 11666606001, 1:5000 dilution), anti-actin (Sangon, D191048, 1:5000 dilution) and anti-α-tubulin (Sigma, T5168, 1:5000 dilution). Horseradish peroxidase-conjugated goat anti-mouse IgG (Sigma, A4416, 1:5000 dilution) was used as the secondary antibody. ECL prime western blot detection reagent (GE Healthcare, RPN2232) was added to the membranes for chemiluminescence detection using Image Lab (Bio-Rad).
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9

Western Blot and Dot Blot Immunoassay Protocol

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For western blots, protein lysates were prepared in 4x loading buffer, heat-denatured at 70°C for 15 minutes. Samples were normalized to equal amounts and resolved on 10% Bis-Tris gels (Thermo Fisher), transferred to 0.44 μm PVDF membranes, and blocked in Licor Odyssey blocking buffer (Licor) for 1 hour. The membrane was incubated overnight at 4°C with primary antibodies diluted in blocking buffer. Secondary antibodies were diluted in blocking buffer and applied to membrane for 1 hour at R.T. Primary antibodies used in immunoblotting experiments included anti-pTDP43 (1:3000, Cosmo Bio), anti-TDP (1:1000, Protein Tech), anti-FLAG (1:1000, Sigma), anti-HA (1:1000, Cell Signaling), and anti-cMyc (1:1000, Roche) For dot blots, 1.5 μL of urea soluble protein fractions were applied to a pre-wetted PVDF membrane and allowed to air dry for ~1.5 hours at R.T. The membrane was blocked in 5% non-fat dry milk for 1 hour and subsequently probed with purified anti-poly(GP) (Rb9258) overnight at 4°C. Raw immunoblot images provided in Figure S14.
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10

Antibody-based Protein Analysis Protocol

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The following antibodies were used: anti-β-actin (Sigma), anti-c-myc (Roche), anti-DMT1 (Abnova), anti-ferroportin (Novus Biologicals, Littleton, CO), anti-GAPDH (Abcam), anti-Parkin clone PRK8 (Covance, Princeton, NJ), anti-α-synuclein (BD Biosciences), anti-TH (Pel-Freez Biologicals, Rogers, AR), anti-transferrin receptor (Abcam) and HRP-conjugated anti-mouse and anti-rabbit (Sigma).
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