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Additional file 3: Cytokine levels in BALF before BLM OA or at 7 or 14 days after BLM OA (n = 5–8 per group). Data are presented as the mean ± SD for normal distribution (IL-13), or as the median with interquartile range for non-normal distribution (TNF-α, IL-4, IL-5, IL-10).

Additional file 9: Lung homogenate was generated from the left lung of mice at 7 days after PBS OA (DAMP- group) or BLM OA (DAMP+ group). Upper inserts (pore size, 0.4 μm; Corning) with cultured lung homogenates were dipped into the basal plate of MSCs (1.0 × 105 cells/well) cultured in DMEM with 10% FBS (S-MSCs) or in serum-free STK2 media (SF-MSCs). After 72 hours, the MSCs were harvested, and intracellular proteins were extracted for TGF-β1 measurement. TGF-β1 was measured using an ELISA kit. Data were calculated as a TGF-β1 per each number of live MSCs in the culture media, and expressed as a percentage of the mean in DAMP- group. Data are presented as means ± SD (n = 3 per group).

Additional file 1: Representative flow cytometry analysis related to the defined positive and negative MSC surface markers on MSCs cultured in DMEM with 10% FBS (S-MSC) or in serum-free STK2 medium (SF-MSC).

Additional file 4: Cytokine levels in serum before BLM OA or at 4, 7, 14, or 21 days after BLM OA (n = 3–7 per group). Data are presented as the median with interquartile range.

Additional file 2: Fluorescence microscopic ex vivo images of engrafted DiI-labeled SF-MSCs (yellow arrows) in murine lungs on the day after injection.

Additional file 10: Representative flow cytometry analysis of the Tregs fraction (red box) in murine blood or lung CD4+ T cells at 6, 10, or 14 days after BLM OA. BLM-administered mice were treated with or without SF-MSC plus Treg depletion Ab (PC61) as shown in Figure 6A.

Additional file 8: S-MSCs or SF-MSCs were seeded into 24-well plates at a density of 5 × 103 cells/well. These MSCs were cultured in serum-free DMEM for 48 h. The supernatants of the culture medium were collected at 6, 12, 24, or 48 h, and the TGF-β1 concentration in the supernatants was measured using an ELISA kit. Data are expressed as concentration of TGF-β1 per each live 100,000 MSCs in the cell culture media. Data are presented as means ± SD (n = 4 per group). On the indicated hours, there was no statistically significant difference in TGF-β1 between the two MSC groups.

Additional file 6: Hydroxyproline levels in the murine left lung at 14 days after BLM OA. At 4 days after BLM OA, mice were further subjected to subcutaneous (sc) or intraperitoneal (ip) administration of SF-MSCs at a dose of 1 × 105 in 100 µL of PBS. Mice without MSC administration were used as controls. Data are presented as the means ± SD (n = 5–8 per group). NS, not significant.

Additional file 7: Representative flow cytometry analysis on engrafted DiI-labeled MSCs in the murine lung. DiI-labeled SF-MSCs were injected into mice subcutaneously (sc) or intraperitoneally (ip) at a dose of 2.0 × 105 cells/mouse in 100 µL of PBS at 4 days after BLM OA. On the day after DiI-labeled SF-MSC injection, MSCs engrafted in murine lungs were measured using flow cytometry.