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Endogenous avidin and biotin were blocked using a specific kit (Zymed).
DNA was extracted from whole blood using a specific kit (DNeasy; Qiagen UK Ltd) and the DNA was tested for the presence of the GYS1 R309H mutation using the restriction fragment polymorphism assay as reported previously [8].
IL-12 levels in BALF were also measured using a specific kit (Ready-set-go, eBioscience Inc).
JNK activity was measured using a specific kit (Cell Signaling Technology) following the manufacturer's instructions and using GST fusion peptide as the specific substrate for JNK.
The concentrations of serum VCA-IgA were determined by enzyme-linked immunoabsorbent assay (ELISA) using a specific kit (Beier, Beijing, China), according to the manufacturers' instruction.
Plasma cytokine and chemokine levels were determined using the ELISA methods described above, whereas the soluble form of CD62L was quantified using a specific kit (cat no. MLS00; R&D Systems).
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Additionally for MECP2 gene we used a specific kit for Rett syndrome that includes probes for MECP2, L1CAM and IRAK1 genes (Salsa P015C, MRC-Holland, Amsterdam, The Netherlands).
Although the use of TaqMan assays provides feasibility to the study and considering that the specificity is extremely high, the exclusion of DNA amplification would be an important factor to address since we have not used a specific kit for miRNA extraction.
Culture media were assayed directly for sRANKL using a specific ELISA kit (Peprotech EC – human sRANKL ELISA development kit), according to the manufacturers directions.
Nitrotyrosine and ADMA were determined using a specific ELISA kit (Chemicon).
Osteocalcin released into the culture media was measured using a specific radioimmunoassay kit (DiaSorin, Stillwater, MN, USA).
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