In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling

Mark G. Carter, Toshio Hamatani, Alexei A. Sharov, Condie E. Carmack, Yong Qian, Kazuhiro Aiba, Naomi T. Ko, Dawood B. Dudekula, Pius M. Brzoska, S. Stuart Hwang, Minoru S.H. Ko

Research output: Contribution to journalArticle

93 Citations (Scopus)

Abstract

Applications of microarray technologies to mouse embryology/genetics have been limited, due to the nonavailability of microarrays containing large numbers of embryonic genes and the gap between microgram quantities of RNA required by typical microarray methods and the miniscule amounts of tissue available to researchers. To overcome these problems, we have developed a microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 22,000 unique mouse transcripts, assembled primarily from sequences of stem cell and embryo cDNA libraries. We have optimized RNA labeling protocols and experimental designs to use as little as 2 ng total RNA reliably and reproducibly. At least 98% of the probes contained in the microarray correspond to clones in our publicly available collections, making cDNAs readily available for further experimentation on genes of interest. These characteristics, combined with the ability to profile very small samples, make this system a resource for stem cell and embryogenomics research.

Original languageEnglish
Pages (from-to)1011-1021
Number of pages11
JournalGenome Research
Volume13
Issue number5
DOIs
Publication statusPublished - 2003 May 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Carter, M. G., Hamatani, T., Sharov, A. A., Carmack, C. E., Qian, Y., Aiba, K., Ko, N. T., Dudekula, D. B., Brzoska, P. M., Hwang, S. S., & Ko, M. S. H. (2003). In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Research, 13(5), 1011-1021. https://doi.org/10.1101/gr.878903