Open Access Highly Accessed Research article

Sequencing the transcriptome of milk production: milk trumps mammary tissue

Danielle G Lemay1*, Russell C Hovey2, Stella R Hartono1, Katie Hinde35, Jennifer T Smilowitz4, Frank Ventimiglia5, Kimberli A Schmidt6, Joyce WS Lee5, Alma Islas-Trejo2, Pedro Ivo Silva1, Ian Korf1, Juan F Medrano2, Peter A Barry6 and J Bruce German4

Author Affiliations

1 Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA

2 Department of Animal Science, University of California Davis, One Shields Ave, Davis, CA 95616, USA

3 Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, MA 02138, USA

4 Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA 95616, USA

5 California National Primate Research Center, University of California Davis, Road 98 and Hutchison Drive, Davis, CA, USA

6 Center for Comparative Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA

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BMC Genomics 2013, 14:872  doi:10.1186/1471-2164-14-872

Published: 12 December 2013



Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, this assay has not been adequately validated in primates. Thus, the objectives of the current study were to assess the suitability of lactating rhesus macaques as a model for lactating humans and to determine whether RNA extracted from milk fractions is representative of RNA extracted from mammary tissue for the purpose of studying the transcriptome of milk-producing cells.


We confirmed that macaque milk contains cytoplasmic crescents and that ample high-quality RNA can be obtained for sequencing. Using RNA sequencing, RNA extracted from macaque milk fat and milk cell fractions more accurately represented RNA from mammary epithelial cells (cells that produce milk) than did RNA from whole mammary tissue. Mammary epithelium-specific transcripts were more abundant in macaque milk fat, whereas adipose or stroma-specific transcripts were more abundant in mammary tissue. Functional analyses confirmed the validity of milk as a source of RNA from milk-producing mammary epithelial cells.


RNA extracted from the milk fat during lactation accurately portrayed the RNA profile of milk-producing mammary epithelial cells in a non-human primate. However, this sample type clearly requires protocols that minimize RNA degradation. Overall, we validated the use of RNA extracted from human and macaque milk and provided evidence to support the use of lactating macaques as a model for human lactation.

Mammary gland; Milk; Rhesus macaque; Human; Transcriptome; RNA-Seq; Milk RNA; Bioinformatics; Milk processing; Transcriptomics