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7 protocols using anti ha tag

1

NLRP3 Inflammasome Activation Assay

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ATP, nigericin, LPS, flagellin and poly(deoxyadenylic-deoxythymidylic) acid sodium salt (poly (dA:dT)) were purchased from InvivoGen (San Diego, USA). DMSO and MG132 was obtained from Sigma-Aldrich (Munich, Germany). MCC950 was purchased from Selleck (Houston, USA). Anti-DYKDDDDK-Tag antibody was purchased from MBL (Beijing, China). Anti-Myc-Tag, anti-HA-Tag and anti-β-actin were purchased from Proteintech (Wuhan, China). Anti-NLRP3, anti-ASC, anti-caspase-1 were obtained from AdipoGen (San Diego, USA). Anti-IL-1β and anti-NEK7 were purchased from Cell Signaling Technology (Danvers, USA). Secondary HRP-conjugated antibodies used were anti-mouse IgG, anti-rabbit IgG (Cell Signaling Technology, Danvers, USA).
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2

ChIP-seq Protocol for BRD4, MED1, H3K27Ac

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ChIP analysis was performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (#38191S, Cell Signaling) following the manufacturer's protocol. An approximate amount of 4 × 106 cells was included in each ChIP reaction mixture. The cells underwent crosslinking with 1% formaldehyde at room temperature for 10 minutes, followed by glycine neutralization for 5 min. Subsequent steps involved resuspending the cells, digesting the chromatin with Micrococcal Nuclease, and sonication to obtain suitable DNA fragments. Dilution of the chromatin complexes occurred in ChIP dilution buffer, and immunoprecipitation was performed using these antibodies: anti-BRD4 (#ab243862, Abcam), anti-MED1 (#ab60950, Abcam), anti-H3K27Ac (#ab4729, Abcam), anti-normal rabbit IgG (#2729S, Cell Signaling), and anti-HA Tag (#66,006–2-lg, Proteintech). Elution of the chromatin from the antibody/protein G magnetic beads utilized ChIP elution buffer and was later transferred to a centrifugation column for DNA purification. Measurement of the immunoprecipitated DNA samples was done through qPCR. The resulting data were presented as a percentage of input DNA. For ChIP-qPCR primer sequences, please refer to  Additional file 1: Table S2.
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3

Antibody-based Signaling Pathway Analysis

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Phospho-CSF1R (Tyr723) (49C10) Rabbit mAb (RRID: AB_2085229), β-catenin (6B3) Rabbit mAb (RRID: AB_331149), anti-Phospho-Akt (Ser473) (RRID: AB_329825) and anti-total-Akt antibodies (RRID: AB_329827) were all bought from Cell Signaling Technology. Anti-GAPDH (RRID: AB_2630358), anti-CSF1R (RRID: AB_2085251), anti-Aβ (MOAB2), anti-β-actin antibodies (RRID: AB_306371) and Alexa Fluor 647 Donkey Anti-Rat IgG H&L (RRID: AB_2813835), as well as the BrdU Cell proliferation ELISA Kit, were all from Abcam. Rat Anti-mouse CD68 monoclonal antibody (RRID: AB_322219) was from Bio-Rad. Anti-HA-tag (RRID: AB_11042321) antibody and anti-Myc-tag antibody (RRID: AB_11182162) were from Proteintech. Rabbit anti-Iba1 (RRID: AB_2687911) was from Wako. Alexa Fluor 488 Goat anti-Rabbit (RRID: AB_10374301), Alexa Fluor 594 Goat anti-Rabbit (RRID: AB_10374440), Alexa Fluor 647 Goat anti-Rabbit antibodies (RRIDAB_10371940) and TRIzol reagent were all from Thermo Fisher Scientific. Granulocyte-macrophage colony stimulating factor (GM-CSF) and CSF1 were from R&D Systems. Basic Glial Cells Nucleofector Kit was purchased from LONZA. ReverTra Ace qPCR RT Master Mix was from TOYOBO. FastStart Universal SYBR Green Master mix was from Roche. CellTiter 96R Aqueous One Solution (MTS assay) and DeadEnd™ Fluorometric TUNNEL System were from Promega.
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4

Protein Expression Analysis in MCF7 Cells

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MCF7 and MCF7/Tam cells were washed with ice-cold PBS for 2 times, and then were added with RIPA lysis buffer. Protein in each sample was analyzed by western blotting as previously reported [7 (link)]. The dilution of each antibodies is: anti-S100A8 (1:500) (Proteintech, Chicago, USA), anti-HRD1 (1:1000) (Abcam, Cambridge, UK), anti-GAPDH (1:4000) (Abcam, Cambridge, UK), anti-HA-tag (1:1000) (Proteintech, Chicago, USA), anti-His-tag (1:1000) (Santz Cruz, CA, USA), anti-Myc-tag (1:1000) (Proteintech, Chicago, USA).
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5

Hepatocyte Cell Culture and Antibody Sourcing

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HepG2 and HEK293T cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% inactivated fetal bovine serum, including penicillin (100 IU/mL) and streptomycin (100 mg/mL) under a 5% CO2 atmosphere at 37°C. PHH cells were pruchased from RILD (Research Institute for liver Diseases, Shanghai, China), HBx antibody (GS968942, Gilead Sciences) was kindly provided as a gift from Dr. Simon Fletcher. The expression constructs of TRIM5γ were generated by cloning the sequence of the coding region into a VR1012 expression vector. Anti-GAPDH antibody, anti-HA-tag, and GST-tag antibody were obtained from Proteintech. Human IFN-α was purchased from Peprotech (Jiangsu, China). DDB1, STAT1, and STAT3 antibodies were procured from Cell Signaling Technology (Danvers, MA, United States). Anti-tubulin antibody was obtained from Santa Cruz Biotechnology (Santa Cruz, CA, United States), Antibodies against TRIM5γ and Smc6 were purchased from Abcam (Shanghai, China), Stattic was obtained from Sigma (Danvers, MA, United States).
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6

Western Blot Immunodetection Protocol

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Western blot was performed as previously reported44 (link). Briefly, the membranes were incubated overnight at 4 °C with the following corresponding primary antibodies: anti-HECTD1 (1:200, Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-HECTD2, anti-HECTD3 (1:800, BIOS, Beijing, China), anti-TRAF3 (1:200, Affinity Biosciences, Shanghai, China), anti-phospho-IKKβ (Tyr199), anti-phospho-IκBα (Ser32/Ser36), anti-phospho-p65 (Ser536) (1:500, Affinity Biosciences, Shanghai, China), anti-IKKβ, anti-IκBα, anti-p65 (1:1000, Proteintech, Wuhan, China), anti-GST tag, anti-His tag, anti-FLAG tag, anti-HA tag (1:5000, Proteintech, Wuhan, China), and anti-β-actin (1:3000, Proteintech, Wuhan, China) antibodies.
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7

Protein Quantification and Antibody Validation

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Protein concentrations were determined using the BCA Protein Assay Kit (Beyotime, P0012). Primary antibodies used in this study are anti-TRIM25 (Proteintech, 12573-1-AP), anti-cleaved PARP (CST, #5625), anti-cleaved Caspase 3 (CST, #9664), anti-EZH2 (CST, #5246), anti-TRAF6 (CST, #8028), anti-Flag tag (Proteintech, 60002-1-Ig), anti-HA tag (Proteintech, 51064-2-AP), anti-His tag (Proteintech, 10001-0-AP), and anti-GAPDH (CST, #5174).
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