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Transcriptome analysis, organ culture methods featured in Cold Spring Harbor Protocols

COLD SPRING HARBOR, N.Y. (Mon., Jan. 3, 2011) -- New technologies and methods are spurring a renaissance in the study of organogenesis. Organogenesis, essentially the process through which a group of cells becomes a functioning organ, has important connections to biological processes at the cellular and developmental levels, and its study offers great potential for medical treatments through tissue engineering approaches. The January issue of Cold Spring Harbor Protocols ( features a method from Washington University's Hila Barak and Scott Boyle ( for "Organ Culture and Immunostaining of Mouse Embryonic Kidneys." The kidney is particularly interesting as it also serves as a model for branching morphogenesis. The protocol describes the isolation, culture and fluorescent immunostaining of mouse embryonic kidneys, and is freely available on the journal's website (

Cap analysis gene expression (CAGE) is a method used to discover new promoters and for quantifying gene activity, providing data essential for studies of regulatory gene networks. But CAGE requires large amounts of RNA, which are often not obtainable from rare specimens. In the January issue of Cold Spring Harbor Protocols ( Piero Carninci and colleagues from the RIKEN Yokohama Institute's Omics Science Center ( present "NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes," a method that can capture information from as little as 10 nanograms of total RNA. The protocol describes how to rapidly prepare nanoCAGE libraries which can be sequenced with high sensitivity. The article is freely available on the journal's website (


Contact: David Crotty
Cold Spring Harbor Laboratory

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