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34 protocols using multiplex assay

1

Measuring Inflammatory Biomarkers in Plasma

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sU, high-sensitivity C-reactive protein (hsCRP), and erythrocyte sedimentation rate (ESR) were measured in standard clinical laboratories. For the measurement of IL-1β, IL-6, and myeloperoxidase (MPO), heparin-anticoagulated blood was centrifuged within 30 min of collection at 3000g for 10 min, and plasma aliquots were stored at − 80 °C until analysis. Plasma interleukin-1β (IL-1β), interleukin-6 (IL-6), and myeloperoxidase (MPO) concentrations were assessed using multiplex assays (Millipore Sigma, Burlington, MA) in duplicate on the MAGPIX multiplex instrument (Luminex Corporation, Austin, TX). Good clinical practices were followed to certify proper storage and daily and long-term quality control of reagents, instruments, and technique.
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2

Multiplex Cytokine Profiling in Longitudinal Study

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Blood samples (10ml) were collected at baseline and at 3 and 6 months for cytokine measurement. Serum was stored in aliquots at −80°C until assayed in batches of 10 to 12. Inflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-1β, IL-10 and IL-17 were measured using commercially available multiplex assays (MilliporeSigma, Burlington, MA). All immunoassays were run in duplicate and read according to manufacturer’s instructions. The investigators performing the cytokine assays were blinded to group assignment.
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3

Colon Tissue Cytokine Profiling

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Colon tissues were washed with phosphate-buffered saline for 6 times to remove faces and microbes, sliced into pieces, then cultured with serum-free RPMI 1640 medium with penicillin (1000 U/mL) and streptomycin (1000 U/mL) for 12 hours. The supernatant was collected by sequential centrifugation at 500 g for 10 minutes and 3000 g for 10 minutes. The levels of IL-1β, TNF-α, IL-6, IL-17A, GM-CSF, LIX, KC, MCP-1, MIP-2, IL-4, IFN-γ, IL-4, IL-5, IL-10, IL-12, and IL-13 were measured by Multiplex Assays according to manufacturer’s instructions (Merck, Darmstadt, Germany).
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4

Cytokine and Chemokine Profiling in BALF

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The concentrations of selected helper T-cell type 1 (Th1), Th2, and Th17 cytokines and chemokines from BALF supernatant were measured with commercially available multiplex assays (EMD Millipore; Billerica, MA). For cytokine/chemokine sample measurements below the lower detection limit, results were assigned a value equal to the minimal detection limit for the specific assay to facilitate statistical analysis of the data.
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5

Serum Biomarkers Measurement Protocol

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Serum alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total bilirubin were measured by standard clinical methods (Yale New Haven Hospital, New Haven, CT). Serum cytokine concentrations were measured by multiplex assays (EMD Millipore, MA).
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Multiplex Profiling of Immunoglobulins and Cytokines

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To verify our most promising proteomics discovery findings, singleplex IgE and multiplex IgG1, IgG2, IgG3, IgG4, IgA and IgM Isotyping assays were performed using Luminex kits (Millipore) according to the manufacturer’s protocol (Figure 1B). The 31 longitudinal plasma samples from the 3 case/control pairs were diluted 1:50 or 1:16,000 for IgE and Isotyping kits, respectively, and added in duplicate on 96 well plates. Multiplex assays (Millipore) for Th1 and Th2 associated cytokines (IFNγ, IL-4, IL-5, IL-6, IL-10, IL-13, GM-CSF, TNF-α, IL-2, IL-12, IL-1β, IL-7, IL-8, IL-17A, IL-21, IL-23, MIP-1α, MIP-1β, MIP-3α, Fractalkine, ITAC) were also performed to further evaluate changes in IgE associated immune markers. Beads were read using a MAGPIX instrument (Millipore) and data were analyzed with Milliplex Analyst software (version 5.1) (Supplemental Methods).
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7

Serum Collection and Cytokine Profiling

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Venous blood was collected onto sterile plastic tubes (BD Vacutainer® SST™ Serum Separation Tubes, Becton-Dickenson; Franklin Lakes, NJ, USA) and allowed to coagulate for 120 min at room temperature before centrifugation (300× g for 10 min) and serum collection. Serum was immediately frozen and stored at −80 °C until analyzed. Repeated freezing and thawing were avoided. The samples were analyzed with Bio-Plex kits for IL-6, IL-11, IL-27(p28), sIL-6R (sCD126), LIF and IL-31 (Bio-Rad, Hercules, CA, USA), and Multiplex Assays (Millipore, Billerica, MA, USA) for CNTF and OSM. All samples were analyzed using Luminex®200™ Bio-Rad platform with program version 6.1 and all analyses were performed in duplicates strictly according to the manufacturer’s instructions. CRP was analyzed using an immunoturbidimetric method provided by Roche (Basel, Switzerland), and during the entire period the lower limit of detection for CRP was 1 mg/L.
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8

Multiplex Serum Biomarker Analysis

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Serum parameters were assessed at 3 months (n=9 per dietary group) and 6 months of age (n=10 per dietary group) using Multiplex assays (Millipore Inc., Billerica, MA, USA) run on a BioRad 200 Bioplex multianalyte detection system (BioRad Inc., Hercules, CA, USA). These subgroups were selected to represent the mean body weight of each dietary group. Serum levels of interleukin (IL)-1α, IL-6, IL-12p70, granulocyte macrophage colony-stimulating factor (GM-CSF) and monocyte chemoattractant protein (MCP)-1 were measured using the mouse cytokine/chemokine magnetic bead panel. Resistin, plasminogen activator inhibitor (PAI)-1, leptin and insulin were measured using the mouse adipokine magnetic bead panel, and adiponectin was measured using a singleplex magnetic bead assay. Serum levels of total insulin-like growth factor (IGF)-1 and IGF-1 binding protein 3 (IGFBP3) levels were measured by ELISA (R&D systems, Minneapolis, MN, USA).
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9

Plasma GLP-1, GIP, and PYY Quantification

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The plasma concentrations of glucagon-like peptide 1 (GLP-1), gastric inhibitory peptide (GIP) and peptide YY (PYY) were determined using multiplex assays (Millipore Corporation).
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10

Cytokine Profiling in Plasma

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Blood samples were obtained and centrifuged immediately to prevent the degradation of complement components, and the plasma was stored at −80°C within 1 h of blood collection. We measured the plasma levels of cytokines and the culture supernatants. We conducted multiple the assay system using Multiplex Assays (Millipore, Billerica, MA) according to the manufacturers' protocols.
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