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5 protocols using ab16898

1

Western Blot Analysis of Cellular Proteins

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Tissue or cellular protein was extracted with 1 × cell lysis buffer (Promega, Madison, WI). Western blot was performed as previously described [9 (link), 11 (link)–15 (link)], with antibodies for HNF4A (ab181604), hexokinase 2 (HK2, ab104836), solute carrier family 2 member 1 (SLC2A1, ab40084), v-myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog (MYCN, ab16898), hnRNPU (ab10297), CTCF (ab188408), clusterin (CLU, ab69644), C-X-C motif chemokine receptor 4 (CXCR4, ab124824), trophoblast glycoprotein (TPBG, ab129058), uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA, ab99323), FLAG (ab125243), Myc (ab9106), glutathione S-transferase (GST, ab19256), histone H3 (ab5103), or β-actin (ab6276, Abcam Inc., Cambridge, MA).
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2

Transient Transformation of G. hirsutum Protoplasts

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Protoplasts were isolated from G.hirsutum cv. YZ1 embryogenic calli (described by Yang et al., 2008 (link)) and transformed with 35S::GhMYB4:MYC constructs. ChIP-based transient expression testing was performed as previously described with minor modification (Lee et al., 2017 (link)). Briefly, protoplasts were fixed with 1% (v/v) formaldehyde for 10 min at room temperature first, and the remaining formaldehyde was neutralized with 0.125-M glycine for 5 min. Fixed protoplasts were collected by centrifuging at 1,000g at 4°C for 5 min. Bioruptor was used at high power with 30-s-on/30-s-off cycles for 15 times until the average chromatin size was approximately 300 bp. Anti-MYC (Abcam, ab16898) antibodies were used to perform immunoprecipitations. Immune complexes were eluted from the protein A or G agarose/salmon sperm DNA beads (Millipore) and reverse cross-linked by incubation for 6 h at 65°C. Then qPCR reactions were performed. The primers are listed in Supplemental Table S5.
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3

Mycn Binding to USP2 Promoter via ChIP

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The binding between Mycn and the USP2 promoter was examined using the ChIP assay kit (P2078, Beyotime). Briefly, the cells were crosslinked in 1% formaldehyde for 10 min and ultrasonicated on ice for chromatin truncation. The cell lysates were reacted with the antibodies of Mycn (1:100, ab16898, Abcam Inc., Cambridge, MA, USA) or IgG (1:100, sc-2025, Santa Cruz Biotechnology, Inc, Santa Cruz, CA, USA). The precipitated immune complexes were collected using agarose magnetic beads, isolated, and de-crosslinked using NaCl at 65℃. The DNA was then extracted and purified using the phenol-chloroform-isoamyl alcohol system, in which the abundance of USP2 promoter fragments was analyzed using qPCR.
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4

Protein Expression Analysis in Tissue Samples

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Total protein was extracted from tissue samples using RIPA lysis buffer (Beyotime Biotechnology) supplemented with Thermo Scientific Halt Protease Inhibitor Cocktail (Thermo Fisher Scientific). Protease inhibitors and phosphatase inhibitors (1:100) were added during protein extraction (MedChemExpress), and a Pierce BCA Protein Analysis Kit (Thermo Fisher Scientific) was used to measure protein concentrations. Protein samples were separated by 10% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride membranes. The membranes were blocked in 5% skim milk and incubated with the respective primary antibodies overnight at 4°C. The samples were incubated with horseradish peroxidase‐conjugated secondary antibodies (1:5000 dilution; Cell Signaling Technology) for 1 h at room temperature, and an iBright FL1500 imaging system (Invitrogen) and Super Signal West Femto Maximum Sensitivity Substrate (Thermo Fisher Scientific, Invitrogen) were used to detect and analyse protein expression levels. Antibody information was provided for anti‐CD44 (60224‐1‐Ig; Proteintech), anti‐MYCN (ab16898; Abcam), and rabbit anti‐glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) (WB: 1/1000; Cell Signaling Technology).
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5

ChIP Antibodies for Transcription Factors

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Antibodies for ChIP were purchased as follows: MYCN (abcam, ab16898), TWIST1 (abcam, ab50887), H3K27Ac (abcam, ab4729), BRD4 (Bethyl, A301-985A), H3K4me3 (EMD Millipore, 07-473), CTCF (EMD Millipore, 07-729), RNA Pol II (Santa cruz, sc-899).
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