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19 protocols using lps ek ultrapure

1

Polarization of Bone Marrow Derived Macrophages

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The BMDMs were detached from the flask using Trypsin-EDTA (Sigma, St. Louis, MO, USA). The cells were seeded in 24-well culturing plates (Sarstedt, Nümbrecht, Germany) at a density 5 × 105 cells/well in DMEM containing 1% FBS and 10,000 I.U./mL PenStrep and rested overnight. For RNA-Seq, BMDMs from five mice were pooled before seeding; for qPCR verification, BMDMs from each individual mouse were seeded separately.
To generate cells with an M1 phenotype, 100 ng/mL of LPS-EK Ultrapure (InvivoGen, Toulouse, France) and 20 ng/mL of IFN-γ (R&D Systems, Minneapolis, MN, USA) were added. frHMGB1 and dsHMGB1 were used at a concentration of 5 µg/mL. LPS-EK Ultrapure (InvivoGen, Toulouse, France) was used at a concentration of 1 µg/mL. PBS was included in all experiments as a control. The BMDMs were stimulated 24 h at 37 °C with 5% CO2 before RNA isolation.
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2

Modulation of B Cell Activation by IFNα

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Naïve B cells were MACS-purified by negative selection from splenocytes of WT, Dnase1l3−/−, Ifnar1−/− or Dnase1l3−/−Ifnar1−/− mice using CD43 microbeads. Purified B cells were labelled with 3 μM Cell trace CFSE (Invitrogen), in PBS+ 2% BSA for 10 mins at RT. CFSE labelled cells were washed twice with PBS and subsequently suspended in RPMI + 10% FBS + 2mM L-glutamine + 10μM β-Mercaptoethanol and plated in round bottom 96 well plates at a concentration of 0.5×106 cells/ well in 200μl media. Cells were either left unactivated or activated with: (1) 5 μg/ml anti-IgM (Jackson Immunoresearch) + anti-CD40 (LEAF-purified, BioLegend) and 5 ng/ml recombinant mouse IL-4 (R&D systems) OR (2) 1μg/ml LPS (LPS-EK Ultrapure, InvivoGen) + 5 ng/ml recombinant mouse IL-4. Unactivated (UA) and activated (A) B cells were supplemented or not with recombinant mouse IFNα1 (BioLegend) at indicated concentrations. B cells were analyzed for activation, proliferation and differentiation after 3 days of culture.
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3

Characterization of Cell Line Cultures

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The cell lines THP-1, SupT1, TZM-bl and H9/HTLV- IIIB along with anti-human APOBEC3G and anti-human APOBEC3F antibody were obtained from the NIH AIDS Research and Reference Reagent Program. THP-1 and Sup T1 were cultured in regular RPMI medium with 10% fetal calf serum (FBS). TZM-bl was grown in DMEM supplemented with 10% fetal calf serum. Immortalized human keratinocytes OKF6/TERT-2, provided by Dr. James G. Rheinwald (Harvard Medical School, MA) [41] (link), were cultured in Keratinocyte-SFM (Invitrogen) supplemented with 0.2 ng/ml recombinant epidermal growth factor (rEGF; Invitrogen), 25 µg/ml bovine pituitary extract (BPE) and 0.4 mM CaCl2 (final). Immortalized human vaginal epithelial cells VK2/E6E7, purchased from ATCC and cultured as described [42] (link). Lipopolysaccharide (LPS-EK Ultrapure) and lipoteichoic acid (LTA-SA) were purchased from Invivogen. MEK inhibitor U0126 was purchased from Calbiochem. Anti p-ERK (E-4) (sc-7383) and anti-ERK2 (D-2) (sc-1647) were purchased from Santa Cruz, USA.
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4

Activation of Human PBMCs by TLR Ligands

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The following TLR ligands (InvivoGen, each 1 µg/mL) were added into wells of 24-well plate containing 1-2 x 106 PBMCs: Poly(I:C) HMW (TLR3), LPS-EK Ultrapure (lipopolysaccharide, TLR4), Imiquimod (IMQ) (R837, TLR7), Resiquimod (R848, TLR7/8), TL8-506 (TLR8), ssRNA40/LyoVec (TLR8) and CpG-ODN (TLR9). The concentration of 1 µg/mL is within the range of manufacturer recommendation and induced maximum cytokine response (not shown) (10 (link), 12 (link)). Golgi plug (1 µl/mL, BD Biosciences) was added to block the cytokines release and cell culture continued for 18h. For some experiments, PBMCs were stimulated with agonists alone or in combination with recombinant human HBsAg subtype adw (10 µg/mL, Fitzgerld) (15 (link)) and PepMix HBV (LEP) Ultra (2 µg/mL, JPT) and cultured for 5 days at 37°C incubator. In experiments for transcription factor induction, cells were re-stimulated with Phorbol-12-myristat-13-acetate (PMA, 50ng/mL) and Ionomycin (Ion, 1 µg/mL) on day 4.
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5

LPS-induced Shock Response in Mice

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WT and RelA/p65Δmye mice received one intra-peritoneal (i.p.) injection of ultra-pure LPS from E. coli K12 (LPS-EK Ultrapure) (InvivoGen, San Diego, CA) (40 mg per kg body weight) diluted in pyrogen-free saline and evidence of LPS-induced shock was examined every 12 hrs. In initial dose response experiments 40mg/kg U-LPS was shown to generate a robust inflammatory response (cytokine production IL-1β, TNF-α and IL-6) in the absence of a rapid shock response in the WT C57BL6 mice. In accordance with CCHMC IACUC-approved protocols, we designated mice as experiencing irreversible LPS-induced shock via the following criteria: hunched posture, lethargy, labored breathing, no righting reflex response, and hypothermic (> 5°C temperature loss). When designated as experiencing LPS-induced shock, mice were immediately euthanized by CO2 inhalation.
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6

Monocyte-Derived Dendritic Cell Activation

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MoDCs were added to 48 well tissue culture plates (105 per well), coated with different doses of LPS-free HMW-2 (10, 1 and 0.1 µg/ml) for 16 h. Cultures were incubated for 2 h and then treated for 4 h with ultrapure E. coli LPS (100 and 10 ng/ml, LPS-100, and LPS-10, LPS-EK Ultrapure from Escherichia coli Invivogen, cat # tlrl-peklps) and supernatants collected for cytokine quantification. Controls were moDCs incubated only with LPS-free HMW-2. Cytokines were quantified using DuoSet ELISA (R&D Systems) and Magnetic luminex assay kits (R&D Systems).
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7

Macrophage Polarization Protocol

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BMDMs were plated non-TC treated multi-well plates (Falcon, Agawam, MA, USA) at a density of 100,000 cells/cm2 and cultured in BMDM media + 20 ng/mL M-CSF. For polarization, cells were stimulated for 24 h with 100 ng/mL lipopolysaccharide (LPS) (LPS-EK Ultrapure, InvivoGen, San Diego, CA, USA) and 10 ng/mL IFN-γ (Peprotech, Rocky Hill, NJ, USA) for M1 profile, or 20 ng/mL IL-4 (Peprotech, Rocky Hill, NJ, USA) for M2 profile.
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8

Screening BMDM Inflammasome Inhibitors

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Bone marrow-derived macrophages were seeded at 50,000 cells per well in BMDM media in tissue-culture coated 96-well plates (Corning, 3596). The next day, cells were pretreated with 200 ng mL−1 of ultrapure E. coli K12 LPS (InvivoGen, LPS-EK Ultrapure) in BMDM media for 3 h. Cells were then washed once with warm PBS and OPTI-MEM containing 40 μM concentration of chemicals from LOPAC library in a 50 μL volume were applied to BMDM for 6 h. For controls, nigericin at 10 μM was applied to control wells of each plate. IL-1β in the supernatants were detected using a mouse IL-1β ELISA kit (Thermo, 88-7013-77) according to manufacturer’s protocol. IL-1β release level of each plate was normalized to within plate nigericin control (set at 2 ng mL−1) as the screen was performed using three different batches of BMDM. All measurements involving BMDM described in the methods include a 3-hour incubation with LPS (‘priming’).
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9

Profiling Immune Cell Responses to Tumor Antigen

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Rabbit anti-human Carcinoembryonic Antigen polyclonal antibody (Ab) (Dako, Denmark Ab A0115); rabbit IgG control (Vector, CA, USA); PE-conjugated anti-CEACAM1 monoclonal antibody (mAb) (R and D Systems MAb2244); FITC-conjugated mouse anti-human CD14 mAb, human FcR Blocking Reagent, CD14+/CD15+ Microbeads and LS columns (Miltenyi biotec, Germany); PE-conjugated mouse anti-human CD86 mAb and PE-Cy7-conjugated mouse anti-human CD80 mAb (Biolegend, CA, USA); PE-conjugated mouse anti-human CD206 mAb and FITC-conjugated mouse anti-human CD15 mAb (Becton Dickinson, CA, USA); PE-conjugated goat anti-rabbit IgG antibody, endotoxin-free water and Histopaque-1077 (Sigma, USA); fixable Vital dye eFluor 780 (ebioscience, CA, USA); LPS-EK Ultrapure (Invivogen, CA, USA); Ni-NTA agarose and polypropylene column (QIAGEN); Pierce BCA Protein Assay Kit and Pierce LAL Chromogenic Endotoxin Quantitation Kit (Thermo Scientific); Proteome Profiler kits (R&D systems, UK). Antiserum to recombinant rD-7 was raised in mice and has been described previously [29] (link).
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10

Whole Blood Cytokine Stimulation Protocol

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Whole blood was collected in heparin containing tubes one hour before surgery (Figure 1). Whole blood samples were processed within 30 minutes of collection. Samples were divided into 1-mL aliquots and incubated at 37 °C for 15 minutes with PBS (control), 100 ng/mL IL-6 (BD Biosciences, San Jose, CA, USA), 100 ng/mL IL-10 (BD Biosciences), a combination of 100 ng/mL IL-2 (BD Biosciences) and 2 ng/mL GMCSF (PeproTech, Rocky Hill, NJ, USA), or 1 µg/mL LPS (LPS-EK Ultra Pure, InvivoGen, San Diego, CA, USA). Blood samples were resuspended in 1.4 mL stabilizing buffer (Smarttube Inc., Palo Alto, CA, USA), incubated for 10 minutes at room temperature for fixation, cooled to 4 °C, and stored at −80 °C until further processing for barcoding and antibody staining.
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