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7 protocols using a7028

1

Immunoprecipitation of His-tagged Proteins

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The cells were lysed in NP-40 lysis buffer (P0013F, Beyotime, Shanghai, China) for 30 min at 4 °C and were clarified by centrifugation at 10,000× g for 15 min at 4 °C to remove cell debris. Then, 80 μL of the supernatant was removed for input sample and the remaining lysate was incubated with 1 μL of the appropriate control mouse IgG (A7028, Beyotime, Shanghai, China) and 20 μL proteinA/G PLUS-Agarose (Santa-Cruz, Dallas, TX, USA) overnight at 4 °C on a flip shaker. Then, the agarose beads were removed by centrifugation and the supernatant was collected and incubated with anti-His antibodies (Proteintech, Rosemont, IL, USA) or TIM-1 polyclonal antibodies for 8 h at 4 °C. Protein A/G PLUS-agarose was then added to the supernatant for about 6 h with a shaker. After conjugation, the beads were washed 4 times with prechilled NP-40 lysis buffer. The agarose beads were resuspended into PBS and 5× loading buffer for Western blotting analysis.
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2

Immunofluorescence analysis of MG-63 cells

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The MG-63 cells in the BioFlex culture plates were fixed with 4% paraformaldehyde for 30 min and subsequently permeabilized with 0.1% Triton X-100 for 5 min. After blocking with 2% goat serum in phosphate-buffered saline (PBS) at 37°C for 1 h, the cells were incubated overnight at 4°C with primary antibodies to Akt (1:400), p-Akt (Thr308; 1:400), mTOR (1:50), p-mTOR (Ser2448; 1:50) and ATP5B (1:50). The cells were then incubated with Alexa Fluor® 488-conjugated goat anti-mouse (A28175) or anti-rabbit (A27034) antibodies (1:400) at 37°C for 1 h, counterstained with 4′,6-diamidino-2-phe-nylindole (DAPI) for 5 min at room temperature and then photographed using a confocal laser scanning microscope (FV1000; Olympus, Tokyo, Japan). The negative controls were incubated with non-immune mouse or rabbit immunoglobulin G (IgG; A7016 and A7028; Beyotime Institute of Biotechnology, Haimen, China) instead of the primary antibodies.
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3

Antibody Validation for Immunological Assays

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The following primary antibodies were used in this study: mouse monoclonal anti-FLAG (M20008; Abmart), mouse monoclonal anti-β-actin (66009-1-lg; Proteintech), rabbit polyclonal anti-TMEM53 (HPA021134; Sigma-Aldrich), mouse monoclonal anti-dsRNA J2 (J2-1702; Scicons), rabbit polyclonal anti-STAT1 (10144-2-AP; Proteintech), mouse monoclonal anti-HA (TA180128; OriGene), rabbit polyclonal anti-HA (H6908; Sigma-Aldrich), and mouse anti-IgG (A7028, Beyotime). Anti-S-tag and anti-NP monoclonal antibodies were prepared in-house. We used the following secondary antibodies: horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG (SA00001-1, Proteintech), HRP-conjugated goat anti-rabbit IgG (SA00001-2, Proteintech), goat anti-mouse IgG H&L DyLight 488 (ab96879, Abcam), goat anti-rabbit IgG H&L Cy3 (ab6939, Abcam), and goat anti-mouse IgG H&L Cy3 (SA00009-1, Proteintech). Universal type I interferon (IFN) (11200, PBL) was acquired from PBL Assay Science.
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4

Investigating Protein-RNA Interactions Using RIP-qPCR

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HEK293T and KYSE150 cells were treated with formaldehyde to cross-link
in vivo protein-RNA complexes. Then, the cells were washed with cold PBS and lysed with RIP buffer at 4°C for 30 min. The cell lysates were incubated overnight with Protein G Sepharose beads (101241; Thermo Fisher) conjugated to antibodies against NPM1 (Ab10530; Abcam) or normal mouse immunoglobulin G (A7028; Beyotime). After the beads were washed several times, the RNA was purified, reverse transcribed into cDNA and detected by qPCR to quantify the binding targets.
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5

ChIP-seq analysis of NRIP1, NSD2, and H3K36me2

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According to the instruction manual of the ChIP kit (Cat. No. 492024, Thermo Fisher Scientific, Rockford, IL, USA), the SCC-9 or CAL27 cells were cross-linked in 1% formaldehyde and ultrasonicated to truncate DNA to 200-500 bp fragments. Thereafter, the lysates were reacted with the antibodies of NRIP1 (customized by Sangon Biotech), NSD2 (1:50, ab75359, Abcam), and H3K36me2 (1:50, ab176921, Abcam) overnight for immunoprecipitation, with normal rabbit IgG (A7016, Beyotime Biotechnology Co., Ltd., Shanghai, China) or normal mouse IgG (A7028, Beyotime) used as the NC antibodies. The DNA in the immunoprecipitated complexes was eluted and purified for qPCR analysis.
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6

Co-Immunoprecipitation of Myc and TFRC

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Conventional co-IP was performed. The antibodies used in co-IP were anti-Myc (1:200 for IP or 1:1000 for IB, 2276 and 5605, CST), anti-TFRC (1:100 for IP or 1:1000 for IB, 13113, CST or ab214039, Abcam) and anti-IgG (A7028 or A7016, 1:50 for IP, Beyotime, Shanghai, China).
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7

Angiotensin II-Induced Vascular Inflammation

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C57BL/6 J wild-type (WT) mice were purchased from the Jackson Laboratory (Sacramento, CA). Male mice (8 weeks old; n = 6 animals per group) were infused with saline or Ang II at a dose of 1000 ng/kg/min (Aladdin, CA) with an osmotic minipump (Alzet MODEL 1007D for 7 days; Alzet MODEL 1002 for 14 days; DURECT, Cupertino, CA) as previously described [3] . A control IgG (A7028, Beyotime, CA) or anti-ICAM-1 neutralizing antibody (BE0020-1, Bio X Cell, USA) was administered every 2 days beginning 1 day before the operation to block soluble ICAM-1 based on our preliminary results and previous publications [16] . The ICAM-1 neutralizing antibody was administrated by tail intravenous injection (IV.). All mice were maintained under specific pathogen-free conditions and provided free access to a normal diet (0.3% sodium chloride). After the study period, the mice were anesthetized, and the serum was collected and aortic tissues were removed and prepared for further molecular and histological examinations. All procedures were approved by the Institutional Animal Care and Use Committee of Dalian Medical University and conformed to the US National Institute of Health's Guide for the Care and Use of Laboratory Animals.
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