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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 (http://cshprotocols.cshlp.org/TOCs/toc1_11.dtl ) features a method from Washington University’s Hila Barak and Scott Boyle (http://devbio.wustl.edu/kopanlab/ ) 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 (http://cshprotocols.cshlp.org/cgi/content/full/2011/1/pdb.5558 ).

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 (http://cshprotocols.cshlp.org/TOCs/toc1_11.dtl ) Piero Carninci and colleagues from the RIKEN Yokohama Institute’s Omics Science Center (http://www.osc.riken.jp/english/ ) 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 (http://cshprotocols.cshlp.org/cgi/content/full/2011/1/pdb.prot5559 ).

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About Cold Spring Harbor Protocols:
Cold Spring Harbor Protocols ( www.cshprotocols.org ) is a monthly peer-reviewed journal of methods used in a wide range of biology laboratories. It is structured to be highly interactive, with each protocol cross-linked to related methods, descriptive information panels, and illustrative material to maximize the total information available to investigators. Each protocol is clearly presented and designed for easy use at the bench—complete with reagents, equipment, and recipe lists. Life science researchers can access the entire collection via institutional site licenses, and can add their suggestions and comments to further refine the techniques.

About Cold Spring Harbor Laboratory Press:
Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York.  Since 1933, it has furthered the advance and spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology.  It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public.  For more information, visit www.cshlpress.com.

For content and submission information:
David Crotty ( crotty@cshl.edu ; 516-422-4007), Executive Editor, Cold Spring Harbor Protocols

For access, subscription, and free trial information:
Stephanie Novara ( novara@cshl.edu ; 516-422-4159), Journals Marketing Manager, CSHL Press

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