Side population (SP) cells are a specialized cell type present at very low numbers in murine bone marrow and other tissues. These cells are considered to be multipotent stem cells capable of differentiating into several cell lineages in vivo and ex vivo. In this report we have isolated SP cells from suspensions of bone marrow of Balb-c mice by using a fluorescence-activated cell sorter (FACS) and we have done the comparative analysis of proteins expressed by the total bone marrow (TBM) and SP cells, by using standard procedures of 2D gel electrophoresis (2DE) followed by MALDI-MS and/or MS/MS. Immunofluorescence analysis of the expression of cytoskeletal proteins actin and vimentin and a multi drug resistance (MDR) family protein ABCG2 were done to further validate the biochemical proteomic data. The classification of the identified proteins into their functional categories indicated that SP cells over express stress proteins, cytoskeletal proteins and enzymes of the glycolytic metabolism. These results could be significant in understanding the physiology of stem cells in the bone marrow.
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