After final purification using magnetic beads, cRNAs were quantified using a NanoDrop and quality checked with Agilent 2100 Bioanalyzer.
The bead center locations were quantified using the imaging system so that the geometry of the porous medium was known very accurately.
Homogenized material was placed on a haemacytometer and beads in the lungs were quantified using epifluorescence microscopic imaging.
Cell-surface antigens on single cells were quantified using standard beads, QIFKIT (Dako Japan, Kyoto, Japan), as described previously [ 35, 36].
Cytokine levels in plasma and culture supernatants were quantified using multiplex bead-based assays (Bio-Plex Cytokine Assays, Bio-Rad Laboratories, Hercules, CA, USA).
Total IgM and IgG isotypes and cytokine/chemokine expression were quantified using Luminex bead-based assays (Affymetrix) and enzyme-linked immunosorbent assays (ELISAs).
The levels of IgG, IgA, and IgM in the serum of the patients directed against the MSCRAMMs, SEs, and immunomodulatory proteins were quantified using a bead-based flow cytometry technique (xMAP, Luminex Corporation).
Proinflammatory cytokines including IL-8, IL-6, IL-1β, and TNF-α in the culture supernatants were quantified using cytometric bead array (CBA) human inflammatory cytokines kit (BD Biosciences, San Jose, USA).
GM-CSF, IL-6, IL-8 and MCP-1 protein levels in cell supernatants were quantified using Cytometric Bead Array (CBA) Flex Sets, an LSRFortessa flow cytometer and FCAP software (all from BD Biosciences) following the manufacturer's instructions.
Cytokines IL-2, IL-4, IL-5, IL-10, IL-12p70, IL-17, TNF- α, and IFN- γ were quantified using Cytometric Bead Array CBA (BD Pharmingen, San Diego, CA, USA) in accordance with the manufacturer's specifications.
