Serum proteomic networks associate with pre-clinical Rheumatoid Arthritis autoantibodies and longitudinal outcomes
48-plex Luminex data after log transformation and main meta data for the manuscript
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Serum proteins were analyzed using a Luminex xMAP 48-plex cytokine/chemokine/growth factor panel (Millipore, HCYTA-60K) which included: IL1A, CXCL1, IFNA2, IFNG, IL1B, CCL3, CCL4, TGFA, TNF, LTA, CXCL9, IL25, PDGFB, FGF2, FLT3LG, CSF3, IL1RN, IL2, IL4, IL5, IL6, IL7, IL8, IL9, IL10, IL12B, IL13, IL15, IL17A, IL17F, IL27, CCL2, CCL7, MCSF, PDGFA, VEGFA, IL12A, CXCL10, IL18, IL22, CCL5, CSF2, IL3, MDC, IL25, CX3CL1, EGF and CD40LG. Standard curves for all analytes were generated using 5-parameter logistic regression on 8 standard samples. Individual analyte sensitivity values are available in the MILLIPLEX® MAP protocol provided with the manufacturer’s kit. Samples were analyzed using a Luminex 200 luminometer and the concentration of analytes was reported in pg/mL. Gene names were used to annotate proteins for readability. Protein expression was log-transformed to normalize, and assessed for distribution/quality control (Figure S1) and proteins (CCL5, CSF2, IL3) were removed if > 25% of the samples fell outside of the assay range.