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Our data confirm previous findings with regards to functional specialization of some organs \u2013 the salivary gland and trachea \u2013 and clarify the embryonic functions of another \u2013 the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. 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