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17 protocols using tlrl peklps

1

In Vitro Cytokine and Cell Death Assays

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For in vitro cytokine determination and LDH assay, BMDMs were seeded at a density of 2 × 105 cells/well in 48-well plates and pre-stimulated with 500 ng ml−1 of LPS (tlrl-peklps; InvivoGen) for 3h, and subsequently infected with CHIKV. The cytokines in the supernatants were measured using a mouse IL-1β ELISA kit (BD Biosciences) according to the manufacturer’s instructions. LDH measurements were performed with CytoTox 96 Non-Radioactive Cytotoxicity Assay (Promega) following the manufacturer’s instructions. The positive control for complete cell lysis and normalization was 9% Triton X-100 (Fisher Scientific); it was incubated with cells for 15 min. The percentage of LDH release was calculated as (mean OD value of sample / mean OD value of Triton X-100 control sample) × 100 and is shown in the figures as the percentage of cell death compared to TritonX-100 (%).
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2

Colipterins Modulate IL-8 Secretion in THP-1 Macrophages

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Human THP-1 (ATCC TIB-202) cells were authenticated and purchased from ATCC, and no mycoplasma contamination was detected according to the manufacturer. The cells were cultured in RPMI medium (Gibco 11875093) with 10% FBS (Sigma F8192–500Ml) and 1% penicillin-streptomycin (Gibco 15070063) and were differentiated into macrophage-like cells by incubation in the presence of 50 nM PMA (Sigma P1585–1MG). Colipterins (17 μM, 1 μM, 0.1 μM, 0.01 μM in DMSO) or DMSO vehicle control (Santa Cruz 202581) were added 1 h prior to differentiation. 100 ng ml−1 LPS (Invivogen tlrl-peklps) were added after 16 h PMA incubation. After 24 h LPS treatment, culture supernatants were collected for IL-8 ELISA assays (R&D DY208–05) according to the manufacturer’s protocol. This assay was performed in triplicates.
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3

Cell Culture and Stimulation Protocols for CRISPRi, MPRA, ATAC-seq, and 4C Experiments

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BJAB (DSMZ, cat. no. ACC 757), Jurkat, Clone E6-1 (ATCC, cat. no. TIB-152), U937 (ATCC, cat. no. CRL-1593.2), THP-1 (ATCC, cat. no. TIB-202), and GM12878 (Coriell, cat. no. GM12878 LCL from B-Lymphocyte) cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% l-glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K and 1M cells/mL. Jurkat T cells were stimulated with 2.5 μg/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 h prior to harvesting for CRISPRi and MPRA, and 1 and 4 h for ATAC-seq experiments. BJAB and GM12878 B cells were stimulated with 2.5 μg/mL of anti-IgM (Sigma-Aldrich, 86620270) and 2 μg/mL anti-CD40 (ThermoFisher, 14-0409-82) for 2 h for CRISPRi and MPRA, and 1 and 4 h for ATAC-seq and 4C (BJAB) experiments. THP-1 and U937 monocytes were stimulated with 100 ng/mL LPS (Invivogen, tlrl-peklps) for 2 h for CRISPRi and MPRA, and 1 and 4 h for ATAC-seq and 4C (U937) experiments.
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4

TLR Agonist-Induced Cytokine Profiling in Dendritic Cells

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CD4 MutuDC2s and MutuDC1s were seeded at a density of 2.5 × 105 cells/cm2 in 96-well or 48-well plates and incubated for 24 h with 450 μL/cm2 of the following TLR agonists diluted in complete medium: Pam3CSK4 (150 ng/mL, tlrl-pms, InvivoGen), poly(I:C) (8.5 μg/mL, tlrl-pic, InvivoGen), LPS from E. coli (100 ng/mL, tlrl-peklps, InvivoGen), ultrapure flagellin from B. subtilis (100 ng/mL, tlrl-pbsfla, InvivoGen), FSL-1 (100 ng/mL, tlrl-fsl, InvivoGen), Gardiquimod™ (1 μg/mL, tlrl-gdqs, InvivoGen), CpG ODN 1826 (1 μM, TriLink BIOTECHNOLOGIES). In all the experiments each condition was plated in technical triplicate. The supernatants were analyzed by ELISA for the presence of IL-6, IL-10, IL-12/IL-23 p40, IL-12p70, and MCP-1(CCL2) using the following kits according to manufacturer's instructions: Mouse IL-6 ELISA Set (555240, BD Biosciences) or Mouse IL-6 ELISA Ready-SET-Go! (88-7064, eBioscience), Mouse IL-10 ELISA Set (555252, BD Biosciences) or Mouse IL-10 (Interleukin-10) ELISA Ready-SET-Go! (88-7104, eBioscience), Mouse IL-12 (p40) ELISA Set (555165, BD Biosciences), Mouse IL-12 (p70) ELISA Set (555256, BD Biosciences), Mouse CCL2 (MCP-1) ELISA Ready-SET-Go! (88-7391, eBioscience).
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5

Whole Blood Cytometry Protocol

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At each study visit, freshly drawn heparinized whole blood underwent red blood cell lysis and cells were fixed (BD biosciences, 558049), either just after blood draw (T0) or after ex vivo stimulation with TLR ligands, including 0.1 μg/ml LPS-EK (TLR4 ligand, InvivoGen, tlrl-peklps), or 5 μg/ml R848 (TLR7/8 ligand, InvivoGen, tlrl-r848), using previously reported methods [41 (link)–43 (link)]. Six hour stimulated samples were designated as T6 PBS, T6 LPS, and T6 R848, respectively. Cells were stored at −80°C until mass cytometry analysis.
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6

Exon Skipping in LPS-Stimulated Lin- BM Cells

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Lin BM cells were exposed to 10 ng/mL LPS (TLRL-PEKLPS, InvivoGen) RNA was extracted to study exon skipping.
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7

PBMC Cytokine Production Assay

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This assay was performed based on NCL method ITA-10 (2015).34 Briefly, human PBMC were re-suspended in a 10% FBS RPMI 1640 medium. Cells (1 x 106/well) were incubated with samples for 24 h at 37°C. Lipopolysaccharides (LPS, tlrl-pekLPS, 20 ng/mL, Invivogen, San Diego, CA, USA) and DPBS were the positive and negative controls, respectively. Following exposure, supernatants were collected and centrifuged at 12,000 RPM for 15 min. Cytokines (TNF-α, IL-1β, IL-6, IL-8, IL-4 and IL-10) were measured with ELISA kits (PeproTech, Rocky Hill, NJ, USA).
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8

Inflammasome Modulation in Cancer Cells

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Human THP-1, U937, HeLa cells, A549, HCT-116, and mouse TRAMP-C2 cells were purchased from ATCC (USA). A549, HeLa and TRAMP-C2 cells were grown in DMEM medium (Invitrogen, USA), while HCT116 cells were cultured in McCoy’s 5A medium (Invitrogen, USA), and both mediums are supplemented with 10% heat-inactivated FCS (Hyclone, USA) and 1% pen/strep (Invitrogen). THP-1 and U937 cells were cultured in RPMI medium (Hyclone, USA) supplemented with 10% heat-inactivated FCS (Hyclone, USA). All cells were grown at 37°C in a humidified 5% CO2 incubator (Thermo Scientific, USA). THP1 cells were differerentiated in PMA (#tlrl-pma, InvivoGen, USA) and stimulated with 1 μg/ml LPS (#tlrl-peklps, InvivoGen, USA) overnight before fresh cell medium was replaced and the cells were either treated with 50% cancer CM or transfected with 1 μg/ml poly (dA:dT) (#tlrl-patc, InvivoGen, USA) with lyovec transfection reagent. Inhibitors THP1 Cells were primed with 100 ng/ml PMA, followed by LPS (1 μg/ml) for 3 hours prior to treatment 1 hour with 1 μg/ml Poly(dA:dT) complexes (AIM2 inflammasome inducer) or A549 tumor CM in the presence of ODN TTAGGG (A151; AIM2 inhibitor, 0.5 μM) or MCC950 (NLRP3 inhibitor, 0.5 μM). Cell supernatants were detected using ELISA.
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9

Purified Bacterial Component Signaling

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Purified flagellin from P. aeruginosa (tlrl-pafla; InvivoGen) and ultrapure LPS from E. coli K-12 (tlrl-peklps; InvivoGen) were resuspended in water. CLI095 (tlrl-cli095; Thermo Fisher Scientific), SB203850 (NC9041893; Fisher), and U0126 (19-147; Sigma) were resuspended in dimethyl sulfoxide.
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10

EV-A71 Infection in Human Cell Lines

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Human rhabdomyosarcoma (RD) cells (ATCC® CCL-136) and SH-SY5Y cells (Procell, #CL-0208) were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, Hyclone) with 100 U/mL penicillin and 100 μg/mL streptomycin. The cells were infected with BrCr strain EV-A71 (ATCC® VR-1432™) or neurotropic strain EV-A71 (Xiangyang-Hubei-09, GenBank accession no. JN230523.1) at the multiplicity of infection (MOI) of 2 or transfected with N-terminal GFP-tagged EV-A71 2A expression plasmid and/or bi-cistronic reporter plasmid containing Cap-Rluc-vIRES-Fluc. Plasmid construction, transcription in vitro and transfection using Lipofectamine 2000 reagent (Life Technologies) were done as previously described [19 (link)]. LPS (#tlrl-peklps, InvivoGen) pre-incubation or post-treatment were specified in figure legends. Observation of cell morphology was performed with microscope. The detail information about cell culture, virus preparation and virus infection and luciferase assay referred to other reports [19 (link)].
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