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5 protocols using anti wdr5

1

RIP Assay for WDR5 Target Identification

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According to the protocol of the Magna RIP kit (Millipore, Billerica, MA, USA), cells were seeded in a plate (15 cm) and transfected with the relevant constructs to overexpress or knock down the target gene. The cells were harvested and lysed with RIP lysis buffer. The magnetic beads were washed with RIP wash buffer, and then, anti-WDR5 (5 µg, Cell Signaling, USA) and anti-IgG antibodies were added and incubated at room temperature for 30 minutes. Total RNA (10 μl, input control) was utilized as a control. Next, RIP was performed, and the samples were incubated in a refrigerator at 4 °C overnight. Subsequently, the incubated samples were washed 5 times with RIP wash buffer. Then, the RNA was extracted and purified by the TRIzol method, and the RNA concentration was measured by a Nanodrop 2000 ultramicroscopy spectrophotometer. Next, the RNA samples were reverse transcribed to cDNA, and expression levels were measured by qRT-PCR.
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2

Immunohistochemical Analysis of GC Tissue

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GC specimens were fixed with 10% formaldehyde and then embedded in paraffin. After preparing 4-μm-thick continuous paraffin sections, immunohistochemistry was performed using anti-VDAC3 (1:200, Proteintech, USA), anti-WDR5 (1:200, Cell Signaling Technology, USA), and anti-FBXW7 (1:300, Proteintech, USA) antibodies. The results were obtained with an automatic digital slide scanning and analysis system (Aperio VERSA 8, Germany), and the immune response score (IRS) was calculated26 (link).
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3

Antibody and Chemical Reagents for Cell Analysis

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The following antibodies were used: anti-Flag (F3165) and anti-β-actin (A1978) (Sigma-Aldrich, St. Louis, MO, USA); anti-GFP (sc-9996) and anti-Lamin A/C (sc-6215) (Santa Cruz biotechnology, Dallas, TX, USA); anti-Tubulin (LF-PA0146A) (AbFrontier, Seoul, Korea); anti-PHF20 (#3934), anti-WDR5 (#13105), and anti-LC3 (#2775) (Cell Signaling Technology, Danvers, MA, USA); anti-HA (#MMS-101R) (Covance, Princeton, NJ, USA); Alexa Fluor 488 donkey anti-rabbit IgG (A21206) and Alexa Fluor 594 donkey anti-mouse IgG (A21203) (Invitrogen, Waltham, MA, USA). The following chemicals were used: hygromycin (H3274), puromycin (P8833), and CQ (C6628) (Sigma-Aldrich, St. Louis, MO, USA); Bafilomycin A1 (#11038) (Cayman, Ann Arbor, MI, USA); and rapamycin (R-5000) (LC laboratories, Woburn, MA, USA).
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4

Nuclear Lysate Preparation for Protein Analysis

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For nuclear lysate preparation, cells were harvested, washed in PBS, and resuspended in Buffer A (10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol and 0.1% Triton) for 8 min on ice. Nuclei were centrifuged at 1300 × g and resuspended again in Buffer A containing benzonase. To prepare whole cell lysates, cells were harvested, washed and re-suspended in RIPA buffer (50 mM Tris (pH 8), 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 0.5% DOC and 1% NP-40) for 30 min on ice. Nuclei were centrifuged at 12 000 RPM, and the supernatant was collected. Protein concentration was determined using the Bradford Assay (Bio-Rad). All capillary electrophoresis runs were normalized to Lamin (anti-Lamin, Cell Signaling 2032) or total protein (Protein Simple). Primary antibodies used include: anti-Treslin (Bethyl A303-472A), anti-MTBP (Santa Cruz, sc-137201), anti-GFP (Abcam, ab290), anti-CUL4B (Sigma, HPA011880), anti-CUL4A (Cell Signaling, 2699), anti-DDB1 (Santa Cruz Biotechnology, SC-137132), anti-CDT2 (Abcam, ab184548), anti-PCNA (Santa Cruz Biotechnology, PC10, sc-56), anti-CDC45L (Protein Tech 15678-1-AP), anti-WDR5 (Cell Signaling, 13105), anti-CDT1 (Abcam, ab202067), anti-p21 (Cell Signaling, 2947) and anti-SET8 (Cell Signaling, 2996). Images were generated with Compass Software (Protein Simple).
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5

Extracting Whole Cell Proteins from C. parvum Infected Cells

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Whole cell extracts were isolated using the standard approach as previously reported (25 (link)). Briefly, cells were grown to 80% confluence and then exposed to C. parvum for various times. Cells were washed with PBS, and the whole cell protein was extracted in M-PER™ Mammalian Protein Extraction Reagent (Thermo Scientific) with proteinase inhibitor according to the product instruction. Protein concentration of each whole cell lysate was determined and subsequently analyzed by Western blot. The following antibodies were used for blotting: anti-H3K4me1 (Abcam), anti-Actin (Sigma), and anti-Wdr5 (Cell Signaling Technology).
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