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4 protocols using sendai virus cantrell strain

1

Modulation of THP-1 Macrophages by Stimuli

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THP-1 cells (ATCC) were cultured in RPMI 1640 (Thermo) supplemented with 10% FCS (R&D) and 1% Pen/Strep (Thermo). LUCAT1−/− THP-1 have been generated previously (10 (link)). Cells were differentiated into macrophage-like cells using 10 ng/mL phorbol-12-myristate acetate (PMA, Sigma) for 24 h, followed by media change and resting in PMA-free medium for another 24 h before stimulation. Cells were treated with 200 ng/mL LPS from E. coli 0111:B4 (Invivogen), Sendai virus Cantrell strain (Charles River Laboratories), 10 ng/mL IFN-α 2b (Gemini), 100 µM to 250 µM 4-octyl itaconate, 250 µM di-methyl itaconate, 5 µM sulforaphane (all Sigma), or 500 nM diABZI-4 (GSK) (19 (link)).
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2

Innate Immune Stimuli Protocols

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Lipopolysaccharide (LPS) and poly-dAdT (pdAdT) were obtained from Sigma-Aldrich and Immunostimulatory DNA oligonucleotides were synthesized as described (8 (link)). Nigericin and ATP were from Invivogen and Sigma respectively. Polyinosinic-polycytidylic acid (poly I:C) was obtained from Invivogen. Sendai virus (Cantrell strain) was purchased from Charles River Laboratories (Wilmington, MA). Lipofectamine 2000® Transfection Reagent was from Invitrogen. GeneJuice was from Novagen (Madison, WI). Universal type I IFN and IFN-γ were from PBL Interferon Source (Piscataway, NJ) and PeproTech (315-05), respectively. S. typhimurium (SL1344 lab strain) was from M. O’Riordan. The plasmids used were p65-pCMV4, c/EBPβ-pcDNA (Addgene), pGL3-enhancer luciferase reporter (Promega). Other plasmids such as Asc in pMSCVneo (Clontech), p205-HA in pRZ-retro, Aim2-FLAG, p204-HA, p205-HA in pEF-BOS or HA-tagged ΔHIN-p205, ΔPYD-p205 and ΔH/ΔP-p205 in pMSCV-PIG (Addgene) were made in the lab.
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3

Inducing Anti-Viral Immune Response in B-Lymphoblasts

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B-Lymphoblasts, GM12878, were obtained from Coriell Institute for Medical Research and cultivated according to the supplier's instructions. Fifteen percent fetal bovine serum was added to Roswell Park Memorial Institute media 1640 (RPMI-1640) with 2 mM L-glutamine for the culture. Sendai Virus (Cantrell strain) obtained from Charles River was used for inducing anti-viral immune response—50 µL of viral stock was added to 1 mL media. Cell samples were taken at 30 min, 1, 2, 4, 6, 12, 18, 24, 48, and 72 h after virus infection for the GRO-seq experiment. For the other experiments, 3C assay and the ChIP-seq experiment, the cells incubated for 6, 12, 18, and 24 h after infection were sampled. Untreated GM12878 cells were used as a control, which is the 0h sample.
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4

Macrophage Activation and NF-κB Inhibition

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Reagents used in the study were obtained from following sources: E. coli LPS was purchased from Sigma-Aldrich (Cat#L2630); recombinant human M-CSF (Peprotech, #300-25), NF-κB inhibitor BAY-7082 (Tocris Bioscience, Cat#1744), Tofacitinib (Sigma, Cat#PZ0017), and HSV-1 (David Knipe Laboratory) Sendai virus (Cantrell strain) were purchased from Charles River Laboratories (Wilmington, MA), GeneJuice was from Millipore, #70967-6. Customized nCounter gene expression code-set was obtained from NanoString technologies (Seattle, WA).
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