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1

Measuring Gene Expression Regulation in Immune Cells

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Electrophoretic mobility shift assays (EMSA) were performed using nuclear extract from Jurkat, LCL, K562, HUVEC cell lines and peripheral blood mononuclear cells (PBMCs) from healthy individuals (supplementary methods). Expression quantitative trait locci (QTLs) were analysed using GTEx datasets,25 (link) and IL19 (R&D Systems), IL10 (Mesoscale Discovery) and aPL levels were measured (supplementary methods).12 (link)
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2

Intradermal LPS Administration Safety and Cytokine Response

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Safety and tolerability were monitored by tracking adverse events, measuring vital signs, and standard laboratory tests (i.e. haematology) at 3, 6, 10, 24 and 48 hours after LPS administration. Circulating cytokines (IL‐1β, IL‐6, IL‐8, IL‐10, IFN‐γ and TNF; Meso Scale Discovery, Rockville, Maryland, USA) were measured in blood samples to detect a possible systemic effect of intradermal LPS administration. The blood samples for cytokine analysis were analysed in 2 batches with each having a different dilution, therefore the lower limit of quantitation (LLOQ) of the samples was the following: IL‐1β 0.298 or 0.745 pg/mL; IL‐6 1.52 or 3.81 pg/mL; IL‐8 1.25 or 3.12 pg/mL; IL‐10 0.702 or 1.76 pg/mL; IFN‐γ 10 or 25 pg/mL; and TNF 0.760 or 1.90 pg/mL.
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BALF Cytokine Profiling via MSD

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The BALF supernatant samples were analysed using MSD pro-inflammatory panel V-Plex including the following analytes: IFN-γ, IL-10, IL-12p70, IL-1β, IL-2, IL-4, IL-5, IL-6, KC/GRO and TNF-α (Meso Scale Diagnostics, Rockville, MD). The analysis was performed according to the manufacturer’s instruction.
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4

Multiplex ELISA for NF-κB Signaling

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Rabbit anti-human phospho p65 NF-κB, PathScan® Signaling Nodes Multi-Target Sandwich ELISA, PathScan® signaling NF-κB ELISA, and PathScan® Sandwich ELISA Lysis Buffer were obtained from Cell Signaling Technology (Pickering, ON, Canada). Cy3-conjugated goat anti-mouse IgG was purchased from Invitrogen Canada (Burlington, ON, Canada). Bordet-Gengou blood agar plates were from BD Biosciences (Mississauga, ON, Canada). Syto9 and Propidium Iodide were from ThermoFisher (Waltham, MA). Wild-type B. pertussis (Tohama I) was propagated at Sanofi Pasteur (Toronto, ON, Canada). Human lung carcinoma epithelial A549 cell line was obtained from ATCC (Old Town Manassas, VA). For the cytokine detection (Eotaxin, Eotaxin-3, IL-10, IL-12/IL-23p40, IL-12p70, IL-13, IL-15, IL-16, IL-17A, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-8 (HA), IL-21, IL-22, IL-23, IL-27, IL-31, IP-10, MCP-1, MCP-4, MDC, MIP-1α, MIP-1β, MIP-3α, TARC, TNF-α, TNF-β, VEGF-A, GM-CSF, and IFN-γ), V-PLEX Human Cytokine 36-Plex Kit (K15089D-2) was used for screening and only 20 selected cytokines were further tested on 20-plex cytokines (Meso Scale Discovery, Rockville, MD).
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