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The analysis of nucleic acids from single cells functioning in their multicellular context is an important part of performing robust developmental genomics studies. Toward this goal, collecting the desired cell(s) from their milieu has been aided by physical means such as laser microdissection. However, tissue processing for laser microdissection has the potential disadvantage of losing molecular information. Procedures involving tissue embedding in plastic have the potential to circumvent these disadvantages, permitting the robust analysis of nucleic acids from single cells isolated from complex tissues.