Additional supporting information available online.

STEM_604_sm_suppinfofig1.eps33622KSupplemental Figure 1. Surface phenotype and multipotent differentiation of luMSC. The lung MSC population can be enriched by flow cytometric sorting of Hoechst 33342 stained lung tissue to identify a CD45neg Hoechstdim side population (SP) of cells. (A) These cells express characteristic cell surface MSC markers (CD73, CD105, CD106, CD 44, CD90, CD133 and Sca1) and lack of hematopoietic and vascular markers, mainly CD45, F480, c-kit and CD146. (B) The luMSC also differentiate into three characteristic mesenchymal lineages, osteoblast, chondrocye and adipocyte, identified by von kossa stain to detect calcium, alizarin red to detect bone matrix, oil red o to distinguish lipid droplets and aggrecan and alcian blue to identify chondrocytes matrix.
STEM_604_sm_suppinfofig2.eps672KSupplemental Figure 2. CD45 positive cells in BAL peak on day 14 following bleomycin injury. Intratracheal bleomycin or PBS was administered to mice and BAL collected on 1,4,7,14 and 35 days post injury. BAL was stained to detect CD45 expressing cells and the mean percentage quantitted by flow cytometry.
STEM_604_sm_suppinfofig3.eps325KSupplemental Figure 3. Proliferating T cells were rarely identified on days 7 following bleomycin injury. Immunoflourescent staining was performed to localize Tcells (CD3) and proliferating cells (PCNA) following bleomycin injury and cell treatment. T cells were present in all bleomycin injured groups however double labeled cells were infrequently identified. Arrows indicate double positive cells.
STEM_604_sm_suppinfofig4.eps4669KSupplemental Figure 4. Validation of gene microarray analysis. Quantitative PCR analysis of select markers of inflammation, angiogenesis, WNT targets and fibrosis in bone marrow (BM 2), bleomycin treated lung (luBleo), luFB and luMSC. Data for each marker were normalized to GAPDH signals.
STEM_604_sm_suppinfofig5.eps617KSupplemental Figure 5. Gating strategy to detect GFP. BM transplants were performed with whole BM from GFP-expressing donor mice. Gates for positive and negative GFP expressing cells were set by the C57Bl6 WT and GFP mouse lung SP and whole lung. Representative scattergrams are shown for each.
STEM_604_sm_suppinfofig6.eps604KSupplemental Figure 6. LacZ staining of donor luMSC and luFB. Donor lung MSC and lung FB were isolated from C57Bl6/ROSAlacZ mice and expanded in culture using chamber slides, fixed with 4% paraformaldehyde for 30 minutes and LacZ staining was performed as previously described (17).
STEM_604_sm_suppinfofig7.eps10855KSupporting Information FIgure 7
STEM_604_sm_suppinfotables.doc275KSupplemental Table 1. Antibodies use in Flow Cytometry Analyses Supplemental Table 2. qPCR Primer Sets Supplemental Table 3. Changes in Gene Expression for luFB vs. luMSC Corresponding to Heatmaps Supplemental Table 4. A Comparison of Gene Expression between BM-MSC, LuMSC and LuFB

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