1 Title: Comprehensive Analysis of Genes Expressed by Rare Microchimeric Fetal Cells in the Maternal Mouse Lung Short Title: Gene Expression of Fetal Cells in Maternal Lung Authors: Stephanie Pritchard 1,2 , Heather C. Wick 3 , Donna K. Slonim 3 , Kirby L. Johnson 1 , Diana W. Bianchi 1,4 1 Mother Infant Research Institute, Floating Hospital at Tufts Medical Center, Boston, Massachusetts; 2 Sackler School of Graduate Biomedical Genetics, Genetics Program, Department of Pathology, Boston, Massachusetts; 3 Department of Computer Science, Tufts University, Medford, Massachusetts; 4 Corresponding author: 800 Washington Street, Box 394, Boston, Massachusetts 02111, dbianchi@tuftsmedicalcenter.org Statement of Advancement of the Field: Comprehensive gene expression microarray analysis of fetal cells isolated from the pregnant murine maternal lung shows the major cell populations to be trophoblasts, mesenchymal stem cells and cells of the immune system. Keywords: Microarray, Microchimerism, Trophoblasts, Mesenchymal Stem Cells, Reproductive Immunology Funding Sources: R01 HD-049469-05 to DWB, T32 HD-049341-05 to DWB, The Provost Fund at Tufts University to DWB, R01 HD-058880 to DKS, Sackler Dean’s Fellowship Award to SP. ABSTRACT During pregnancy, cells from each fetus travel into the maternal circulation and organs, resulting in the development of microchimerism. Identification of the cell types in this microchimeric population would permit better understanding of possible mechanisms by which they affect maternal health. However, comprehensive analysis of fetal cells has been hampered by their rarity. In this study, we sought to overcome this obstacle by combining flow cytometry BOR Papers in Press. Published on June 6, 2012 as DOI:10.1095/biolreprod.112.101147 Copyright 2012 by The Society for the Study of Reproduction.