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Therefore, a comprehensive characterization of these processes relies on efficient methods to isolate each of the different cell types throughout male gametogenesis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed stable transgenic<jats:italic>Arabidopsis<\/jats:italic>lines and reliable purification tools based on Fluorescence-Activated Cell Sorting (FACS) in order to isolate highly pure and viable fractions of each cell\/nuclei type before and after pollen mitosis. In the case of mature pollen, this was accomplished by expressing GFP and RFP in the sperm and vegetative nuclei, respectively, resulting in 99% pure sorted populations. Microspores were also purified by FACS taking advantage of their characteristic small size and autofluorescent properties, and were confirmed to be 98% pure.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We provide simple and efficient FACS-based purification protocols for<jats:italic>Arabidopsis<\/jats:italic>microspores, vegetative nuclei and sperm cells. This paves the way for subsequent molecular analysis such as transcriptomics, DNA methylation analysis and chromatin immunoprecipitation, in the developmental context of microgametogenesis in<jats:italic>Arabidopsis<\/jats:italic>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1746-4811-8-44","type":"journal-article","created":{"date-parts":[[2012,10,17]],"date-time":"2012-10-17T22:30:45Z","timestamp":1350513045000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":84,"title":["FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei"],"prefix":"10.1186","volume":"8","author":[{"given":"Filipe","family":"Borges","sequence":"first","affiliation":[]},{"given":"Rui","family":"Gardner","sequence":"additional","affiliation":[]},{"given":"Telma","family":"Lopes","sequence":"additional","affiliation":[]},{"given":"Joseph P","family":"Calarco","sequence":"additional","affiliation":[]},{"given":"Leonor C","family":"Boavida","sequence":"additional","affiliation":[]},{"given":"R Keith","family":"Slotkin","sequence":"additional","affiliation":[]},{"given":"Robert A","family":"Martienssen","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg D","family":"Becker","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,10,17]]},"reference":[{"issue":"5\u20136","key":"213_CR1","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1387\/ijdb.052019lb","volume":"49","author":"LC Boavida","year":"2005","unstructured":"Boavida LC, Becker JD, Feijo JA: The making of gametes in higher plants. 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