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9 protocols using anti myc antibody sc 40

1

Antibody Characterization for Protein Study

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The antibodies used in this study were anti-Myc antibody (sc-40, Santa Cruz), anti-HA antibody (sc-57592, Santa Cruz), anti-HBO1 antibody (sc-13284, Santa Cruz), anti-DDB2 antibody (sc-81246, Santa Cruz), anti-XPC antibody (sc-30156, Santa Cruz), anti-TFIIH p89 antibody (sc-293, Santa Cruz), anti-CPD antibody (NMDND001, Cosmo Bio), anti-Orc2 antibody (sc-13238, Santa Cruz), anti-acetyl-Histone H4 antibody (#06-866 Millipore), anti-Histone H4 antibody (ab10158, Abcam), anti-acetyl-Histone H3K14 antibody (A-4023, EPIGENTEK), anti-Histone H3 (tri methyl K4) antibody (ab1012, Abcam), anti-Histone H3 antibody (39763, ACTIVE MOTIF), anti-γH2AX antibody (50-171-736, Upstate), anti-SNF2H antibody (ab3749, Abcam), anti-ACF1 antibody (NB100-61041, Novusbio), anti-CSB antibody (553C5a, BIO MATRIX RESEARCH), anti-UVsS-A antibody (H00057654-B01, Abnova) and anti-β-actin antibody (sc-47778, Santa Cruz). Phospho Ser50 and Ser53 HBO1 rabbit polyclonal antibodies were generated by immunization with a synthetic phosphopeptide (CSARLpSQSpSQD). To perform immunoprecipitation of GFP-SNF2H, anti-GFP mAb-Agarose (D153-8, MBL) was used.
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2

SLAT-IP3R1 Interaction Regulation

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Cells were stimulated as described earlier and were lysed in 1% NP-40, 150 mM NaCl, 50 mM tris (pH 7.4), 10 mM NaF, 1 mM phenylmethyl-sulfonyl fluoride (PMSF), aprotinin (10 μg/ml), and leupeptin (10 μg/ml). Lysates were collected after centrifugation at 13,000g for 10 min. Immunoprecipitation was performed by adding the antibodies indicated in the figure legends with 30 μl of protein G–Sepharose (GE Healthcare Life Sciences) and incubating the lysates overnight at 4°C. Samples were washed four times with lysis buffer, and the immunoprecipitates were dissolved in 1× Laemmli buffer, subjected to SDS-PAGE, transferred onto a nitro-cellulose membrane, and analyzed by Western blotting with an anti-FLAG M2 mAb (F3165, Sigma), anti-Myc antibody (sc-40, Santa Cruz Bio-technology Inc.), or anti-Xpress antibody (R910-25, Life Technologies). To assess the effect of the TAT fusion proteins on the SLAT-IP3R1 interaction, cells were prestimulated for 72 hours, rested overnight in medium containing IL-2 (20 U/ml), and then cross-linked with anti-TCR/CD28 mAbs after a 1.5-hour incubation with the indicated TAT fusion proteins in RPMI 1640 containing 0.5% FBS at 37°C.
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3

Analyzing Myc-DACT1 Binding to DVL2

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To analyze binding of wildtype and mutant Myc-DACT1 to Flag-DVL2 (dishevelled segment polarity protein 2) by immunoprecipitation (IP), HEK293T cells (1.0 × 107) were seeded in Petri dishes and transiently co-transfected with pcDNA3.1-Myc-DACT1 (wildtype or mutant) and pCMV5-Flag(3x)-DVL2 (#24802; Addgene, Watertown, MA, USA). At 24 h post transfection, cells were lysed in IP buffer (50 mM Tris-HCl, pH 8.0, 50 mM sodium fluoride, 1 mM sodium orthovanadate, 1% Triton X-100) supplemented with protease and phosphatase inhibitors (Roche Diagnostics, Mannheim, Germany). After adding 1 µg of anti-Myc antibody (#sc-40; Santa Cruz Biotechnology, Dallas, TX, USA), lysates were rotated overnight at 4 °C. Protein G Sepharose beads (GE, Boston, MA, USA) were equilibrated in IP buffer and incubated with the lysates for 4 h at 4 °C. After washing 5 × with IP lysis buffer, proteins eluted from the beads using Laemmli buffer (62.5 mM Tris-HCl, pH 6.8, 10% glycerin, 2% sodium dodecyl sulfate (SDS), 5% 2-mercaptoethanol, 1 mM ethylenediaminetetraacetic acid, 0.01% bromophenol blue) were detected by Western blot analysis.
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4

Immunoprecipitation of Myc-tagged proteins

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293T or RPE1 cells were lysed in ELB buffer (50 mM Hepes pH 7, 150 mM NaCl, 5 mM EDTA pH 8, 0.1% NP-40, 1 mM DTT, 0.5 mM AEBSF, 2 µg/ml leupeptin, 2 µg/ml aprotinin, 10 mM NaF, 50 mM β-glycerophosphate, and 10% glycerol) on ice for 10 min, lysates were centrifuged at 16,000×g for 15 min, and supernatants were incubated with 2 µg anti-Myc antibody (sc-40, Santa Cruz) and 15 µl Protein G Sepharose (17-0618-01, GE Healthcare) or 15 µl Flag beads (A2220, Sigma-Aldrich). For immunoprecipitation, 2 mg of the resulting supernatant was immunoprecipitated, and beads were washed with ELB buffer and analyzed by immunoblotting. Protein band intensities were quantified using Image J software. The uncropped blots are shown in Supplementary Fig. 6.
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5

Proteomic Analysis of ABCA8 Interactome

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Human glial (oligodendrocytic) hybrid cell line (MO3.13: Cedarlane, ON, Canada) stably expressing myc-BirA-ABCA8-v5 was generated by lentiviral transduction and selected with 1.0 μg/ml puromycin. The myc-BirA∗-fusion construct was expressed upon induction with doxycycline for at least 6 days prior to analysis. Induction was verified by Western blotting using an anti-myc antibody (sc40; Santa Cruz, Dallas, TX). 50 μM biotin was added to the medium for 24 h prior to cell lysis under denaturing conditions (M-lysis buffer; Roche, Basel, Switzerland). Control cells not induced with doxycycline or without addition of biotin were processed in parallel. Biotinylated proteins were purified using streptavidin-coupled magnetic beads (Invitrogen). After reduction and alkylation, purified proteins were separated by 4–12% NuPage Novex Bis-Tris gels (Invitrogen), stained with Colloidal Blue (Invitrogen), and digested in-gel using trypsin (27 (link)).
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6

FOCAD Interacts with Tubulin Isoforms

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Binding of FOCAD to HSP90AB1 was verified using 6xHis-tag-mediated pull down as detailed in Supplementary material online resource. Binding of FOCAD to tubulin isoforms was assayed using Myc-tag-mediated pull down. HEK293T cells were transiently cotransfected with constructs expressing N-terminal Myc-tagged TUBA1A, TUBB3, TUBB6 or TUBG1 and untagged FOCAD. At 24 h post transfection, cells were washed with ice-cold phosphate-buffered saline (PBS) and lysed for 30 min on ice in 1 ml of immunoprecipitation (IP) lysis buffer (20 mM Tris-HCl, pH 8.0), 50 mM sodium fluoride, 1 mM sodium orthovanadate, 1% Triton X-100, supplemented with protease and phosphatase inhibitors (Roche Diagnostics)). Cell lysates were incubated with 1 µg of anti-Myc antibody (sc-40; Santa Cruz Biotechnology, Dallas, TX, USA) by tumbling over night at 4°C. Protein G Sepharose beads (GE Healthcare, Little Chalfont, UK) were equilibrated in IP lysis buffer, blocked with 0.1% bovine serum albumin (BSA; Thermo Fisher Scientific) and incubated with the lysates for 4 h at 4°C. After five washing steps with IP lysis buffer, bound protein was eluted from the beads using Laemmli buffer (62.5 mM Tris-HCl, pH 6.8, 10% glycerol, 2% SDS, 5% 2-mercaptoethanol, 1 mM EDTA, 0.01% bromophenol blue), and detected by Western blot analysis.
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7

Evaluation of Apoptosis and Oxidative Stress

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Anti‐Myc (#sc‐40) antibody was purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Anti‐HIF‐1α (#36169) was purchased from Cell Signaling Technology (Danvers, MA, USA). Anti‐β‐actin (#AC026) was purchased from ABclonal Company (Wuhan, China). Dual‐luciferase reporter assay system (#E194A) was purchased from Promega (Madison, WI, USA). 3‐TYP (#S8628) and NAC (#S1623) were purchased from Selleck (Houston, TX, USA). FITC‐Annexin V Apoptosis Detection Kit I (#556547) was purchased from BD Pharmingen (San Diego, CA, USA). CM‐H2DCFDA (#C6827) and MitoSOX™ Red (# M36008) were purchased from Thermo Fisher (Waltham, MA, USA). Annexin V‐FITC Apoptosis Detection Kit (#C1062) was purchased from Beyotime (Shanghai, China).
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8

HIF-1α Regulation by Ubiquitin Pathway

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Antibodies including anti-OTUB1 (#3783), anti-HIF-1α (#36169), anti-VHL (#68547), anti-FIH (#4426), anti-Ubiquitin (#3936), anti-K48-linkage Specific Polyubiquitin (#8081), and normal rabbit IgG (#2729) were purchased from Cell Signaling Technology. Anti-ACTB (#AC026) antibody was purchased from ABclonal. Anti-Flag (#F1804) antibody was purchased from Sigma. Anti-HA (#901515) antibody was purchased from Covance. Anti-Myc (#SC-40) antibody was purchased from Santa Cruz Biotechnology. CoCl2 (#C8661), Deferoxamine mesylate salt (DFX) (#D9533), DMOG (#D3695) and MG-132 (#474790) were purchased from Sigma. FG4592 (#S1007) was purchased from Selleck. The cells were treated with DMOG (1 mM) or FG4592 (up to 100 μM) for 6–8 h, and DMSO was used as a control.
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9

Antibody Reagents for Protein Analysis

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Antibodies including anti-OTUB1 (#3783), anti-SET7 (#2825), anti-His (#9991), anti-Histone H3 (#4499), anti-UBC13 (#6999), anti-HA (#3724), anti-Ubiquitin (#3936), and normal rabbit IgG (#2729) were purchased from Cell Signaling Technology. anti-OTUB1 (#ab270959) and anti-SET7 (#ab124708) antibodies were purchased from Abcam. Anti-β-actin (#AC026) antibody was purchased from ABclonal. Anti-Flag (#F1804) antibody was purchased from Sigma. anti-HA (#901515) antibody was purchased from Covance. Anti-Myc (#SC-40) antibody was purchased from Santa Cruz Biotechnology. Anti-α-tubulin (#62204) and Alexa Fluor 488 goat anti-rabbit IgG (#A11008) were purchased from Thermo Fisher Scientific. Erastin (#HY-15763) was purchased from MCE. TBH solution (#B802372) was purchased from Macklin. CHX (#HY-12320) was purchased from MCE.
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